From J.C.Wojdel at tnw.tudelft.nl Fri Aug 1 14:52:09 2003 From: J.C.Wojdel at tnw.tudelft.nl (Jacek Wojdel) Date: Fri, 1 Aug 2003 14:52:09 +0200 Subject: [CPMD-list] Charges and population analysis. In-Reply-To: ; from hutter@pci.unizh.ch on Thu, Jul 31, 2003 at 01:42:15PM +0200 References: <20030728193011.A3555@dct7243.dct.tudelft.nl> Message-ID: <20030801145209.A22188@dct7243.dct.tudelft.nl> On Thu, Jul 31, 2003 at 01:42:15PM +0200, Juerg Hutter wrote: > Hi > > I was running a simple test case (water dimer) with USPP's and got > reasonable results for both, Hirschfeld and ESP charges. > There must be something special with your input I can't reproduce. > Hi, Firstly thanks for replying. Secondly, I prepared a test case that exhibits the problem: ### Begin input ### &CPMD OPTIMIZE WAVEWUNCTION pROPERTIES CALCULATION rESTART WAVEFUNCTION COORDINATES LATEST LSD &END &SYSTEM SYMMETRY 2 POINT GROUP AUTO ANGSTROM SCALE CARTESIAN CELL ABSOLUTE DEGREE 10.22 10.22 10.22 90.00 90.00 90.00 CUTOFF 30. MULTIPLICITY 3 &END &ATOMS *Fe_ps.uspp BINARY NEWF LMAX=2 2 0.00 0.00 0.00 0.50 0.00 0.00 *C_ps.uspp BINARY NEWF LMAX=2 6 0.20 0.00 0.00 -0.20 0.00 0.00 0.00 0.20 0.00 0.00 -0.20 0.00 0.00 0.00 0.20 0.00 0.00 -0.20 *N_ps.uspp BINARY NEWF LMAX=2 6 0.30 0.00 0.00 -0.30 0.00 0.00 0.00 0.30 0.00 0.00 -0.30 0.00 0.00 0.00 0.30 0.00 0.00 -0.30 &END &DFT FUNCTIONAL PW91 GC-CUTOFF 1.D-5 &END &PROPERTIES CHARGES pROJECT WAVEFUNCTION pOPULATION ANALYSIS MULLIKEN &END ### End input ### The output of charges calculation contains: *********************************************************************** ATOM COORDINATES CHARGES X Y Z INT ESP 1 Fe 0.0000 0.0000 0.0000 8.000 11.481 2 Fe 9.6565 0.0000 0.0000 8.000 4.383 3 C 3.8626 0.0000 0.0000 4.000 -2.612 4 C -3.8626 0.0000 0.0000 4.000 -2.518 5 C 0.0000 3.8626 0.0000 4.000 -2.518 6 C 0.0000 -3.8626 0.0000 4.000 -2.612 7 C 0.0000 0.0000 3.8626 4.000 -2.518 8 C 0.0000 0.0000 -3.8626 4.000 -2.612 9 N 5.7939 0.0000 0.0000 5.000 -0.045 10 N -5.7939 0.0000 0.0000 5.000 -0.113 11 N 0.0000 5.7939 0.0000 5.000 -0.113 12 N 0.0000 -5.7939 0.0000 5.000 -0.045 13 N 0.0000 0.0000 5.7939 5.000 -0.113 14 N 0.0000 0.0000 -5.7939 5.000 -0.045 *********************************************************************** > If you don't specify a basis, CPMD will use a default Slater type basis > with exponents from the Slater rules or where available from the > Clementi set. > If you want to specify your own basis the input strongly depends on > the type of basis functions you want to use. That would be great (I don't need to have any real values, just some general information about the electronic structure at the moment). Unfortunately, activating the population analysis in the above input file gives: **************************************************************** * PROPERTY CALCULATIONS * **************************************************************** RV30| WARNING! NO WAVEFUNCTION VELOCITIES RESTART INFORMATION READ ON FILE ./RESTART.1 *** PHFAC| THE NEW SIZE OF THE PROGRAM IS 48096 kBYTES *** LSCR= 100 MAX(LRNLSM1,LRNLSM2) = 30180 PROGRAM STOPS IN SUBROUTINE RNLSM| SCRATCH ARRAY TOO SMALL FORTRAN STOP 999 Life's tough... I'm probably doing something stupid here, but I can't figure out what yet. Just in case anyone wonders, I'm using Fe,C,N uspps generated with no changes from 7.3.4 version of Vanderbilt code. Greetings, Jacek -- +-------------------------------------+ |from: J.C.Wojdel | | J.C.Wojdel at tnw.tudelft.nl | +-------------------------------------+ From deubel at cscs.ch Sun Aug 3 16:49:08 2003 From: deubel at cscs.ch (Dirk V. Deubel) Date: Sun, 3 Aug 2003 16:49:08 +0200 (MET DST) Subject: [CPMD-list] PhD student positions, CSCS/ETH Zurich Message-ID: PhD Student Position in Interdisciplinary Computational Science at the Swiss Center for Scientific Computing, ETH Zurich, Lugano, Switzerland Research topics: (A) Medicinal Chemistry. To understand the molecular mechanism of the anticancer drug cisplatin, [PtCl2(NH3)2], we study its reaction with potential biological targets using quantum chemical methods. Our long-term goal is a contribution to the development of novel metallopharmaceuticals. (B) Industrial Oxygen Transfer Catalysis. This project aims to improve and develop catalytic processes for the oxidation of hydrocarbons. Parts of the work are performed in collaboration with experimentalists. Job environment: Our institute provides excellent knowledge, resources, and service for high performance computational science. Successful candidates receive their PhD from the Swiss Federal Institute of Technology, ETH Zurich. Our institute is located close to Lugano in the Ticino province, which offers a pleasant culture, beautiful scenery, and excellent opportunities for outdoor activities. Candidates: You are an enthusiastic and creative scientist and have a Master of Science, Diploma, or a similar university degree in chemistry, biology, pharmacology, or medicine. You belong to the top 20 percent of your age group. Experience in computational science can be helpful. You would like to explore a new interdisciplinary research field and you are interested in international collaborations. Applications: Please send your application by fax to Dirk V. Deubel, +41-91-610-8282, including your CV, names and addresses of 1-2 references, brief summaries of your former projects, preferred research topic (A) or (B), preferred starting date. Links: My research interests: http://staff-www.uni-marburg.de/~deubel Our institute: http://www.cscs.ch ETH Zurich: http://www.ethz.ch Dirk V. Deubel Swiss Center for Scientific Computing, CSCS Swiss Federal Institute of Technology, ETH Zrich CH-6928 Manno TI Switzerland Phone: +41-91-610-8280 E-mail: deubel at cscs.ch From mkosmows at mailbox.syr.edu Mon Aug 4 13:21:13 2003 From: mkosmows at mailbox.syr.edu (mkosmows) Date: Mon, 4 Aug 2003 07:21:13 -0400 Subject: [CPMD-list] Trying to get MPI to work Message-ID: <3F2E428A@OrangeMail> Dear CPMD community: I am trying to implement MPI for the first time. I will try to give as much information as possible, so excuse both the length of this post as well as any incompleteness. My goal is to make a very small cluster of two Athlon PC's. They are both Athlon 1.3GHz processors with 1Gb RAM each, but have different motherboards and video cards. I am using PGI f77 and GNU C compilers. I am attempting to compile the latest 3.7.2 code and have not tried any previous versions of the code for MPI. I am trying to implement the mpich 1.2.5 from Argonne. The installation of mpi on my compiler machine seems to have gone well. I set FC=pgf77, and that works properly as I had initially a flexlm error (due to infrequent use of the pgf77 I always forget to turn on the license). There are two current issues: the mpi test fails, and I am unable to compile CPMD using the mpi configure option. The compile failure will be discussed first. I used Configure PC-PGI-MPI. I changed only the FFLAG option of -pc64 to -pc 64 (perhaps this could be fixed in the distributed Configure script in future distributions). The error I get is undefined reference to `mpi_xxxx in function my_xxx within mypara.o. There are several of these errors. Any assistance would be greatly appreciated. Lastly, I get the following error message when attempting to run the suggested test of mpich. I think it has something to do with ssh. I have made the ssh keys on both systems, and made sure that both systems have each others public keys. I have added the proper hostnames to the mpich machine config file on the system running the test. I have also made sure that the ssh server allows empty passwords. Please forgive the lack of proper terminology - first time with ssh. [mark at linux test]$ make testing (cd pt2pt ; ./runtests -check ) Failed to run simple program! Output from run attempt was *** Testing Unexpected messages *** bash: line 1: /home/mark/mpich-1.2.5/examples/test/pt2pt/./third: No such file or directory p0_7921: p4_error: Child process exited while making connection to remote process on linux2: 0 /home/mark/mpich-1.2.5/bin/mpirun: line 1: 7921 Broken pipe /home/mark/mpich-1.2.5/examples/test/pt2pt/./third -p4pg /home/mark/mpich-1.2.5/examples/test/pt2pt/PI7836 -p4wd /home/mark/mpich-1.2.5/examples/test/pt2pt *** Testing Unexpected messages *** mpirun program was /home/mark/mpich-1.2.5/bin/mpirun mpirun command was /home/mark/mpich-1.2.5/bin/mpirun -mvhome -np 2 ./third >third.out 2>&1 make: *** [runtest] Error 1 [mark at linux test]$ Any insight on either of these problems would be greatly appreciated. If further information is required, I will provide as best as possible. Thank you, Mark Kosmowski Chemistry Department Syracuse University mkosmows at syr.edu From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Mon Aug 4 19:12:34 2003 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Mon, 04 Aug 2003 19:12:34 +0200 Subject: [CPMD-list] Trying to get MPI to work In-Reply-To: Your message of "Mon, 04 Aug 2003 07:21:13 EDT." <3F2E428A@OrangeMail> Message-ID: <200308041712.h74HCYL29464@yello.theochem.ruhr-uni-bochum.de> >>> "MK" == mkosmows writes: MK> Dear CPMD community: MK> The compile failure will be discussed first. I used Configure PC-PGI-MPI. I MK> changed only the FFLAG option of -pc64 to -pc 64 (perhaps this could be MK> fixed in the distributed Configure script in future distributions). The error MK> I get is MK> undefined reference to `mpi_xxxx in function my_xxx within mypara.o. There MK> are MK> several of these errors. Any assistance would be greatly appreciated. hi mark, the default configure uses the options '-byteswapio' and '-Msecond_underscore'. you should remove them for your setup. the second option is for g77 compatibility and you don't need this, if you have compiled your mpi library with pgf77 (or pgf90). MK> Lastly, I get the following error message when attempting to run the suggested MK> test of mpich. I think it has something to do with ssh. I have made the ssh MK> keys on both systems, and made sure that both systems have each others MK> public keys. I have added the proper hostnames to the mpich machine config MK> file on the system running the test. I have also made sure that the ssh MK> server MK> allows empty passwords. Please forgive the lack of proper terminology - first MK> time with ssh. MK> [mark at linux test]$ make testing MK> (cd pt2pt ; ./runtests -check ) MK> Failed to run simple program! MK> Output from run attempt was MK> *** Testing Unexpected messages *** MK> bash: line 1: /home/mark/mpich-1.2.5/examples/test/pt2pt/./third: No such file MK> or MK> directory MK> p0_7921: p4_error: Child process exited while making connection to remote MK> process on linux2: 0 stupid question: did you make sure, that mpich uses ssh and not rsh? also the test seems to assume, that both machines have a (NFS-)shared directory and the test starts from that. is that true? hope this helps, axel. MK> /home/mark/mpich-1.2.5/bin/mpirun: line 1: 7921 Broken pipe MK> /home/mark/mpich-1.2.5/examples/test/pt2pt/./third -p4pg MK> /home/mark/mpich-1.2.5/examples/test/pt2pt/PI7836 -p4wd MK> /home/mark/mpich-1.2.5/examples/test/pt2pt MK> *** Testing Unexpected messages *** MK> mpirun program was /home/mark/mpich-1.2.5/bin/mpirun MK> mpirun command was MK> /home/mark/mpich-1.2.5/bin/mpirun -mvhome -np 2 ./third >third.out 2> &1 MK> make: *** [runtest] Error 1 MK> [mark at linux test]$ MK> Any insight on either of these problems would be greatly appreciated. If MK> further MK> information is required, I will provide as best as possible. MK> Thank you, MK> Mark Kosmowski MK> Chemistry Department MK> Syracuse University MK> mkosmows at syr.edu MK> _______________________________________________ MK> CPMD-list mailing list MK> CPMD-list at cpmd.org MK> http://www.cpmd.org/mailman/listinfo/cpmd-list -- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From m.t.storr at reading.ac.uk Tue Aug 5 15:06:37 2003 From: m.t.storr at reading.ac.uk (M.T.Storr) Date: Tue, 5 Aug 2003 14:06:37 +0100 (BST) Subject: [CPMD-list] Ultrasoft Pseudopotentials Message-ID: Hi, I have a somewhat bizarre question relating to CPMD. I have recently downloaded CPMD and notice that it can use ultrasoft pseudopotentials. I am also awaiting the release of the latest version of Castep. I am aware of calculations using Castep/USP's on my system that give good results. I would however like to try to carry out some calculations using CPMD due to the nature of its availability. I was therefore wondering if CPMD will read the USP's that come with Castep or if anyone has a way to convert them. Sorry for the obscure question. Thanks Mark ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Mark T. Storr School of Chemistry University of Reading PO Box 224 Whiteknights Reading Berkshire RG6 6AD E-mail: M.T.Storr at reading.ac.uk Tel: +44 (0)118 9875123 Ext. 7415 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From mkosmows at mailbox.syr.edu Wed Aug 6 02:39:20 2003 From: mkosmows at mailbox.syr.edu (mkosmows) Date: Tue, 5 Aug 2003 20:39:20 -0400 Subject: [CPMD-list] Trying to get MPI to work Message-ID: <3F326138@OrangeMail> Dear CPMD community: I have gotten the MPI version of CPMD 3.7.2 (PGI f77, GCC cc) to run. However, I get an error, described below. I am running MPICH 1.2.5 and CPMD 3.7.2. I have not tried other versions of CPMD. I am using a "cluster" of two Athlon 1.3GHz workstations with 1Gb RAM each. Both computers are running Mandrake 9.1 linux. In the terminal where the program was running: [mark at linux SP]$ mpirun -np 2 ~/work/bin/cpmd.x BH3NH3.in >BH3NH3.out p4_error: latest msg from perror: No route to host Killed by signal 2. /home/mark/work/mpich-1.2.5/bin/mpirun: line 1: 8167 Broken pipe /home/mark/work/bin/cpmd.x "BH3NH3.in" -p4pg /home/mark/work/cpmd/BH3NH3/lda/25K8.8.8/SP/PI8082 -p4wd /home/mark/work/cpmd/BH3NH3/lda/25K8.8.8/SP [mark at linux SP]$ mpirun -np 2 ~/work/bin/cpmd.x BH3NH3.in >BH3NH3.out p4_error: latest msg from perror: No route to host Killed by signal 2. /home/mark/work/mpich-1.2.5/bin/mpirun: line 1: 10028 Broken pipe /home/mark/work/bin/cpmd.x "BH3NH3.in" -p4pg /home/mark/work/cpmd/BH3NH3/lda/25K8.8.8/SP/PI9943 -p4wd /home/mark/work/cpmd/BH3NH3/lda/25K8.8.8/SP [mark at linux SP]$ And in the output file: NFI GEMAX CNORM ETOT DETOT TCPU 1 2.112E-01 1.667E-02 -29.677204 0.000E+00 88.83 2 1.074E-01 6.307E-03 -31.056725 -1.380E+00 90.80 3 4.252E-02 2.703E-03 -31.253852 -1.971E-01 91.64 4 3.083E-02 1.413E-03 -31.281939 -2.809E-02 93.56 p0_10028: (5378.632967) net_send: could not write to fd=5, errno = 113 p0_10028: p4_error: net_send write: -1 The first time this happened, only two lines after the NFI line were printed. Also, the second workstation (not the one that mpirun ... cpmd.x was invoked on) stops giving a video signal and is unresponsive to ssh or webmin from the first workstation. Is this something that mpi is doing, or should I be looking for a hardware problem? Thank you, Mark Kosmowski Chemistry Department Syracuse University mkosmows at syr.edu From mkosmows at mailbox.syr.edu Wed Aug 6 06:48:20 2003 From: mkosmows at mailbox.syr.edu (mkosmows) Date: Wed, 6 Aug 2003 00:48:20 -0400 Subject: [CPMD-list] Re: Help getting MPI to work Message-ID: <3F33163B@OrangeMail> Dear CPMD communtiy: I just got that same broken pipe error when using my notebook as the second processor, so I am inclined to rule out hardware problem. However, the notebook did not hang and is still perfectly functional. I will try using both desktops and the notebook together to see what will happen. Hopefully someone knows what to do. Thank you, Mark Kosmowski Chemistry Department Syracuse University mkosmows at syr.edu From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Wed Aug 6 12:44:23 2003 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Wed, 06 Aug 2003 12:44:23 +0200 Subject: [CPMD-list] Trying to get MPI to work In-Reply-To: Your message of "Tue, 05 Aug 2003 20:39:20 EDT." <3F326138@OrangeMail> Message-ID: <200308061044.h76AiN629069@yello.theochem.ruhr-uni-bochum.de> >>> "MK" == mkosmows writes: MK> Dear CPMD community: hello mark, MK> I have gotten the MPI version of CPMD 3.7.2 (PGI f77, GCC cc) to run. MK> However, I get an error, described below. I am running MPICH 1.2.5 and MK> CPMD 3.7.2. I have not tried other versions of CPMD. I am using a "cluster" MK> of two Athlon 1.3GHz workstations with 1Gb RAM each. Both computers are MK> running Mandrake 9.1 linux. MK> In the terminal where the program was running: MK> [mark at linux SP]$ mpirun -np 2 ~/work/bin/cpmd.x BH3NH3.in >BH3NH3.out MK> p4_error: latest msg from perror: No route to host MK> Killed by signal 2. MK> /home/mark/work/mpich-1.2.5/bin/mpirun: line 1: 8167 Broken pipe MK> /home/mark/work/bin/cpmd.x "BH3NH3.in" -p4pg MK> /home/mark/work/cpmd/BH3NH3/lda/25K8.8.8/SP/PI8082 -p4wd MK> /home/mark/work/cpmd/BH3NH3/lda/25K8.8.8/SP MK> [mark at linux SP]$ mpirun -np 2 ~/work/bin/cpmd.x BH3NH3.in >BH3NH3.out MK> p4_error: latest msg from perror: No route to host that means, that your second machine has crashed hard. this is most likely due to an overloading of the memory management (tcp/ip is very tough on the mm-subsystem) or the ethernet driver (some of them are pretty fragile). also some gcc versions occasionally miscompile some parts of the kernel or the drivers. what kernel version are you using (cat /proc/version)? and what ethernet card(s) do you have (/sbin/lspci -v | grep -A6 Ether)? MK> Killed by signal 2. MK> /home/mark/work/mpich-1.2.5/bin/mpirun: line 1: 10028 Broken pipe MK> /home/mark/work/bin/cpmd.x "BH3NH3.in" -p4pg MK> /home/mark/work/cpmd/BH3NH3/lda/25K8.8.8/SP/PI9943 -p4wd MK> /home/mark/work/cpmd/BH3NH3/lda/25K8.8.8/SP MK> [mark at linux SP]$ MK> And in the output file: MK> NFI GEMAX CNORM ETOT DETOT TCPU MK> 1 2.112E-01 1.667E-02 -29.677204 0.000E+00 88.83 MK> 2 1.074E-01 6.307E-03 -31.056725 -1.380E+00 90.80 MK> 3 4.252E-02 2.703E-03 -31.253852 -1.971E-01 91.64 MK> 4 3.083E-02 1.413E-03 -31.281939 -2.809E-02 93.56 MK> p0_10028: (5378.632967) net_send: could not write to fd=5, errno = 113 MK> p0_10028: p4_error: net_send write: -1 MK> The first time this happened, only two lines after the NFI line were printed. MK> Also, MK> the second workstation (not the one that mpirun ... cpmd.x was invoked on) MK> stops giving a video signal and is unresponsive to ssh or webmin from the MK> first MK> workstation. Is this something that mpi is doing, or should I be looking for MK> a MK> hardware problem? well, it may also be a hardware problem (wrong bios settings, weak memory, etc.). you may want to run memtest on all machines to rule out weak memory. MK> Thank you, MK> Mark Kosmowski MK> Chemistry Department MK> Syracuse University MK> mkosmows at syr.edu >>> "MK" == mkosmows writes: MK> Dear CPMD communtiy: MK> I just got that same broken pipe error when using my notebook as the second MK> processor, so I am inclined to rule out hardware problem. However, the MK> notebook did not hang and is still perfectly functional. hmm, another question: do you use direct cabeling or a switch or a hub? if it is one of the latter two, you may want to look up the switch statistics for the ports you are using (if you have access to that info, that is). perhaps there is a cabeling problem. please also look at the output of 'netstat -i'. it should produce something like this (gigabit ethernet machine, uptime 9 days): Kernel Interface table Iface MTU Met RX-OK RX-ERR RX-DRP RX-OVR TX-OK TX-ERR TX-DRP TX-OVR Flg eth0 1500 0 2147483647 0 0 0 2147483647 1 0 0 BRU lo 16436 0 1837 0 0 0 1837 0 0 0 LRU or this (100mbit ethernet machine, uptime 9 days): Kernel Interface table Iface MTU Met RX-OK RX-ERR RX-DRP RX-OVR TX-OK TX-ERR TX-DRP TX-OVR Flg eth0 1500 0 935317809 0 0 58 915489568 0 0 0 BRU lo 16436 0 26270 0 0 0 26270 0 0 0 LRU both machines have been heavily used for tcp/ip based parallel jobs. hope this helps, axel. MK> I will try using both desktops and the notebook together to see what will MK> happen. Hopefully someone knows what to do. MK> Thank you, MK> Mark Kosmowski MK> Chemistry Department MK> Syracuse University MK> mkosmows at syr.edu MK> _______________________________________________ MK> CPMD-list mailing list MK> CPMD-list at cpmd.org MK> http://www.cpmd.org/mailman/listinfo/cpmd-list -- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From masroor.bangesh at uni-jena.de Wed Aug 6 12:55:59 2003 From: masroor.bangesh at uni-jena.de (Masroor Ahmad) Date: Wed, 06 Aug 2003 12:55:59 +0200 Subject: [CPMD-list] Problem in subroutine SOLVE References: <200308061001.MAA22346@cpmd.org> Message-ID: <3F30DEBF.7060007@uni-jena.de> Hi list, I got the following message while trying to converge wavefunction in an geometry optimization step. What could be the reason for SOLVE to halt? Thanks. **************************************************************** *** TOTAL STEP NR. 65 GEOMETRY STEP NR. 1 *** *** GNMAX= 6.591946E-02 ETOT= -169.812863 *** *** GNORM= 2.024372E-02 DETOT= 0.000E+00 *** *** CNSTR= 0.000000E+00 TCPU= 392.46 *** **************************************************************** 1 8.530E-03 2.847E-03 -169.524733 2.881E-01 6.56 2 5.646E-03 6.238E-04 -169.790442 -2.657E-01 5.18 3 3.581E-03 3.392E-04 -169.810740 -2.030E-02 4.21 4 5.103E-03 2.220E-04 -169.813858 -3.118E-03 3.51 5 3.609E-03 1.262E-04 -169.816197 -2.339E-03 3.69 6 3.205E-03 8.779E-05 -169.816788 -5.913E-04 3.76 7 1.721E-03 5.533E-05 -169.817167 -3.789E-04 3.78 8 1.144E-03 4.078E-05 -169.817307 -1.399E-04 4.02 9 7.509E-04 3.076E-05 -169.817391 -8.437E-05 4.81 10 4.298E-04 2.363E-05 -169.817447 -5.511E-05 7.32 11 3.966E-04 1.847E-05 -169.817486 -3.992E-05 5.96 12 3.295E-04 1.527E-05 -169.817506 -1.983E-05 5.58 13 2.318E-04 1.257E-05 -169.817520 -1.383E-05 4.08 14 1.670E-04 1.024E-05 -169.817532 -1.157E-05 3.91 15 1.032E-04 8.411E-06 -169.817539 -7.721E-06 3.86 16 9.595E-05 6.966E-06 -169.817545 -5.455E-06 3.84 17 9.209E-05 5.941E-06 -169.817549 -3.711E-06 3.88 18 7.854E-05 5.117E-06 -169.817551 -2.726E-06 3.88 19 8.320E-05 4.460E-06 -169.817553 -1.946E-06 3.97 20 7.177E-05 3.886E-06 -169.817555 -1.531E-06 3.88 SOLVE! INFO= 10 PROGRAM STOPS IN SUBROUTINE SOLVE| DO NO SUCCEEDED IN SOLVING [PROC= 0] -- Your's truly Masroor Ahmad -------------------------------------------------| Institute f?r Anorganische und Analytische Chemie| Friedrich-Schiller Universit?t Jena | Carl-Zeiss Promenade 10 | D-07743 Jena (Germany) | -------------------------------------------------| Tel: +49(0)3641-644028 | Fax: +49(0)3641-644036 | Mob: +49(0)1798880964 | -------------------------------------------------| Residence: | Apartment 605,Am Herrenberg 11 | 07745 Jena (Germany) | -------------------------------------------------| From masroor.bangesh at uni-jena.de Wed Aug 6 13:11:09 2003 From: masroor.bangesh at uni-jena.de (Masroor Ahmad) Date: Wed, 06 Aug 2003 13:11:09 +0200 Subject: [CPMD-list] Another message while converging wavefunczion References: <200308061001.MAA22346@cpmd.org> Message-ID: <3F30E24D.2000800@uni-jena.de> Dear All, After restarting from ealier run which failed in subroutine SOLVE,,,(my previuos message to list)..now I got another failure in UNIV. I'm trying to optimize structure of 16 atoms molecule in 0 SYMMETRY and a cell size 9.2 1 1.Plane wave energy cutoff I used is 40 ryd. and using Goedecker type PP for C,H,V,N and O. Thanks **************************************************************** *** TOTAL STEP NR. 77 GEOMETRY STEP NR. 2 *** *** GNMAX= 5.209175E-02 [7.26E-02] ETOT= -172.086977 *** *** GNORM= 1.547440E-02 DETOT= -1.905E-03 *** *** CNSTR= 0.000000E+00 TCPU= 84.73 *** **************************************************************** 1 1.093E-02 2.440E-03 -171.931822 1.552E-01 2.36 2 6.392E-03 5.844E-04 -172.072745 -1.409E-01 2.36 3 5.461E-03 3.172E-04 -172.082256 -9.511E-03 2.38 4 4.407E-03 1.979E-04 -172.084799 -2.543E-03 2.40 5 5.013E-03 1.176E-04 -172.085981 -1.182E-03 2.43 6 4.041E-03 8.228E-05 -172.086368 -3.869E-04 2.44 7 2.033E-03 5.608E-05 -172.086585 -2.176E-04 2.46 UNIV| THE LEADING MINOR OF ORDER 1 IS NOT POSITIVE DEFINITE, UNIV| AND THE FACTORIZATION COULD NOT BE COMPLETED. PROGRAM STOPS IN SUBROUTINE UINV| ILLEGAL RESULTS DPOTRF [PROC= 0] -- Your's truly Masroor Ahmad -------------------------------------------------| Institute f?r Anorganische und Analytische Chemie| Friedrich-Schiller Universit?t Jena | Carl-Zeiss Promenade 10 | D-07743 Jena (Germany) | -------------------------------------------------| Tel: +49(0)3641-644028 | Fax: +49(0)3641-644036 | Mob: +49(0)1798880964 | -------------------------------------------------| Residence: | Apartment 605,Am Herrenberg 11 | 07745 Jena (Germany) | -------------------------------------------------| From mkosmows at mailbox.syr.edu Thu Aug 7 18:01:43 2003 From: mkosmows at mailbox.syr.edu (mkosmows) Date: Thu, 7 Aug 2003 12:01:43 -0400 Subject: [CPMD-list] Trying to get MPI to work Message-ID: <3F3642BB@OrangeMail> Dear Dr. Kohlmeyer: I am using a 10/100 cable router/switch for my network backbone. I am planning to invest in a gigabit network in a month or two, as well as purchasing some additional hardware, but wanted to get MPI running on my current equipment before spending money. It looks like there may only be a 10Mb ethernet card in the machine that crashed - but my notebook has a 10/100 on-board NIC, and while the notebook didn't crash, mpirun cpmd did. I have attached the results of all of the tests you reccomended below in the file testresults. I ran memtest86 2.9 on both desktop machines and no errors after 2 passes. Any advice would be greatly appreciated. Even if it is only to tell me that the problem will go away with server level equipment. Have a good day, and thank you very much for your help and concern, Mark Kosmowski >===== Original Message From axel.kohlmeyer at theochem.ruhr-uni-bochum.de ===== >>> "MK" == mkosmows writes: > >MK> Dear CPMD community: > >hello mark, > >MK> I have gotten the MPI version of CPMD 3.7.2 (PGI f77, GCC cc) to run. >MK> However, I get an error, described below. I am running MPICH 1.2.5 and >MK> CPMD 3.7.2. I have not tried other versions of CPMD. I am using a "cluster" >MK> of two Athlon 1.3GHz workstations with 1Gb RAM each. Both computers are >MK> running Mandrake 9.1 linux. > >MK> In the terminal where the program was running: > >MK> [mark at linux SP]$ mpirun -np 2 ~/work/bin/cpmd.x BH3NH3.in >BH3NH3.out >MK> p4_error: latest msg from perror: No route to host >MK> Killed by signal 2. >MK> /home/mark/work/mpich-1.2.5/bin/mpirun: line 1: 8167 Broken pipe >MK> /home/mark/work/bin/cpmd.x "BH3NH3.in" -p4pg >MK> /home/mark/work/cpmd/BH3NH3/lda/25K8.8.8/SP/PI8082 -p4wd >MK> /home/mark/work/cpmd/BH3NH3/lda/25K8.8.8/SP >MK> [mark at linux SP]$ mpirun -np 2 ~/work/bin/cpmd.x BH3NH3.in >BH3NH3.out >MK> p4_error: latest msg from perror: No route to host > >that means, that your second machine has crashed hard. >this is most likely due to an overloading of the memory >management (tcp/ip is very tough on the mm-subsystem) >or the ethernet driver (some of them are pretty fragile). >also some gcc versions occasionally miscompile some parts of >the kernel or the drivers. > >what kernel version are you using (cat /proc/version)? >and what ethernet card(s) do you have (/sbin/lspci -v | grep -A6 Ether)? > >MK> Killed by signal 2. >MK> /home/mark/work/mpich-1.2.5/bin/mpirun: line 1: 10028 Broken pipe >MK> /home/mark/work/bin/cpmd.x "BH3NH3.in" -p4pg >MK> /home/mark/work/cpmd/BH3NH3/lda/25K8.8.8/SP/PI9943 -p4wd >MK> /home/mark/work/cpmd/BH3NH3/lda/25K8.8.8/SP >MK> [mark at linux SP]$ > >MK> And in the output file: > >MK> NFI GEMAX CNORM ETOT DETOT TCPU >MK> 1 2.112E-01 1.667E-02 -29.677204 0.000E+00 88.83 >MK> 2 1.074E-01 6.307E-03 -31.056725 -1.380E+00 90.80 >MK> 3 4.252E-02 2.703E-03 -31.253852 -1.971E-01 91.64 >MK> 4 3.083E-02 1.413E-03 -31.281939 -2.809E-02 93.56 >MK> p0_10028: (5378.632967) net_send: could not write to fd=5, errno = 113 >MK> p0_10028: p4_error: net_send write: -1 > >MK> The first time this happened, only two lines after the NFI line were printed. >MK> Also, >MK> the second workstation (not the one that mpirun ... cpmd.x was invoked on) >MK> stops giving a video signal and is unresponsive to ssh or webmin from the >MK> first >MK> workstation. Is this something that mpi is doing, or should I be looking for >MK> a >MK> hardware problem? > >well, it may also be a hardware problem (wrong bios settings, weak >memory, etc.). you may want to run memtest >on all machines to rule out weak memory. > >MK> Thank you, > >MK> Mark Kosmowski > >MK> Chemistry Department >MK> Syracuse University >MK> mkosmows at syr.edu > > >>> "MK" == mkosmows writes: > >MK> Dear CPMD communtiy: > >MK> I just got that same broken pipe error when using my notebook as the second >MK> processor, so I am inclined to rule out hardware problem. However, the >MK> notebook did not hang and is still perfectly functional. > >hmm, another question: do you use direct cabeling or a switch or a hub? >if it is one of the latter two, you may want to look up the switch >statistics for the ports you are using (if you have access to that info, >that is). perhaps there is a cabeling problem. please also look at the output of >'netstat -i'. it should produce something like this (gigabit ethernet >machine, uptime 9 days): > >Kernel Interface table >Iface MTU Met RX-OK RX-ERR RX-DRP RX-OVR TX-OK TX-ERR TX-DRP TX-OVR Flg >eth0 1500 0 2147483647 0 0 0 2147483647 1 0 0 BRU >lo 16436 0 1837 0 0 0 1837 0 0 0 LRU > >or this (100mbit ethernet machine, uptime 9 days): >Kernel Interface table >Iface MTU Met RX-OK RX-ERR RX-DRP RX-OVR TX-OK TX-ERR TX-DRP TX-OVR Flg >eth0 1500 0 935317809 0 0 58 915489568 0 0 0 BRU >lo 16436 0 26270 0 0 0 26270 0 0 0 LRU > >both machines have been heavily used for tcp/ip based parallel jobs. > >hope this helps, > axel. > >MK> I will try using both desktops and the notebook together to see what will >MK> happen. Hopefully someone knows what to do. > >MK> Thank you, > >MK> Mark Kosmowski > >MK> Chemistry Department >MK> Syracuse University >MK> mkosmows at syr.edu > >MK> _______________________________________________ >MK> CPMD-list mailing list >MK> CPMD-list at cpmd.org >MK> http://www.cpmd.org/mailman/listinfo/cpmd-list > > > >-- > >======================================================================= >Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de >Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 >Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 >D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de >======================================================================= >If you make something idiot-proof, the universe creates a better idiot. Chemistry Department Syracuse University mkosmows at syr.edu -------------- next part -------------- A non-text attachment was scrubbed... Name: testresults Type: application/octet-stream Size: 2298 bytes Desc: not available Url : http://cpmd.org/pipermail/cpmd-list/attachments/20030807/08abb672/attachment.obj From mkosmows at mailbox.syr.edu Fri Aug 8 07:59:34 2003 From: mkosmows at mailbox.syr.edu (mkosmows) Date: Fri, 8 Aug 2003 01:59:34 -0400 Subject: [CPMD-list] Continued saga of trying to get MPICH to work Message-ID: <3F391076@OrangeMail> Dear CPMD community: I have managed to get mpirun cpmd to work successfully with a small test case. However, despite TESR=8, the output file states that a supercell of 17*17*17 unit cells was used. Why is this? Thank you, Mark Kosmowski Chemistry Department Syracuse University mkosmows at syr.edu From Ari.P.Seitsonen at iki.fi Fri Aug 8 13:04:25 2003 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Fri, 8 Aug 2003 13:04:25 +0200 Subject: [CPMD-list] Continued saga of trying to get MPICH to work In-Reply-To: <3F391076@OrangeMail> (message from mkosmows on Fri, 8 Aug 2003 01:59:34 -0400) References: <3F391076@OrangeMail> Message-ID: <200308081104.h78B4Pt05073@magadino.cscs.ch> Dear Mark, > I have managed to get mpirun cpmd to work successfully with a small > test case. However, despite TESR=8, the output file states that a > supercell of 17*17*17 unit cells was used. Why is this? That's eight translations in the negative side, eight in the positive side plus the zero translation, i.e. 8+8+1 = 17 (e.g. R_1 = A_1 * i1, i1 = -8..+8, A_1 = the first basis vector, R_1 = the translation, i1 = an index). Greetings, apsi PS Please remember to keep TESR so large only with very small unit cells -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland From cpmd at kressworks.com Sun Aug 10 01:20:42 2003 From: cpmd at kressworks.com (CPMD) Date: Sat, 9 Aug 2003 23:20:42 +0000 Subject: [CPMD-list] MPI and SMP on P4 Linux using PGI compilers Message-ID: <200308092320.43048.cpmd@kressworks.com> When I do # Configure to get a list of target platforms, I see PC-PGI PC-PGI-MPI PC-PGI-MPI-QMMM PC-PGI-QMMM PC-IFC-MPI PC-IFC and IBM-SP3 IBM-SP3-SMP IBM-SP4 IBM-SP4-SMP IBM-SP4-64 IBM-SP4-SMP-64 but no SMP for PC-PGI. Is SMP supported on Linux PCs using Reh Hat 7.3 and PGI compilers? How about PC-PGI-MPI-SMP? Thanks. Jim Kress From jimkress at kressworks.com Sun Aug 10 18:48:20 2003 From: jimkress at kressworks.com (Jim Kress) Date: Sun, 10 Aug 2003 16:48:20 +0000 Subject: [CPMD-list] version 3.7.2 compileing with PGF for MPI Message-ID: <200308101648.21203.jimkress@kressworks.com> I am using the PGI 4.2-1Workstatoion compiler set to make CPMD v3.7.2. When I compile CPMD v3.7.2 using: # ./Configure PC-PGI > Makefile # make Where I have removed the references to '-byteswapio' and '-Msecond_underscore', the make process completes with pgf77-Warning-Unknown switch: -pc64 and gives me a cpmd.x executable which runs the test cases just fine. However, when I compile using: # ./Configure PC-PGI-MPI > Makefile # make I get the following output: rm -f cpmd.f /lib/cpp -P -C -traditional -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT -DPARALLEL -DMP_LIBRARY=__MPI -DMYRINET ./cpmd.F ./cpmd.f mpif77 -c -fast -Mr8 -pc64 -Msignextend ./cpmd.f -o ./cpmd.o f77: unrecognized option `-pc64' f771: Unrecognized option `-fast' In file included from ./cpmd.f:11: system.h: In subroutine `cpmd': system.h:76: POINTER (IP_NKPBL,NKPBL),(IP_KPBEG,KPBEG) 1 2 Unrecognized statement name at (1) and invalid form for assignment or statement-function definition at (2) system.h:183: POINTER (IP_MAPGP,MAPGP) 1 2 Unrecognized statement name at (1) and invalid form for assignment or statement-function definition at (2) system.h:195: POINTER(IP_IATPT,IATPT),(IP_IPEPT,IPEPT),(IP_IATPE,IATPE) 1 2 Unrecognized statement name at (1) and invalid form for assignment or statement-function definition at (2) system.h:473: POINTER (IP_NASSEL,NASSEL) 1 2 Unrecognized statement name at (1) and invalid form for assignment or statement-function definition at (2) In file included from ./cpmd.f:13: prop.inc:52: POINTER (IP_ICUBEORB,ICUBEORB),(IP_Z_11,Z_11) 1 2 Unrecognized statement name at (1) and invalid form for assignment or statement-function definition at (2) system.h:77: COMMON/NKIP/ IP_NKPBL,IP_KPBEG 1 How do I fix this? Thanks. Jim From jimkress at kressworks.com Sun Aug 10 19:50:13 2003 From: jimkress at kressworks.com (Jim Kress) Date: Sun, 10 Aug 2003 17:50:13 +0000 Subject: [CPMD-list] version 3.7.2 compileing with PGF for MPI Message-ID: <200308101750.13696.cpmd@kressworks.com> I am using the PGI 4.2-1Workstatoion compiler set to make CPMD v3.7.2. When I compile CPMD v3.7.2 using: # ./Configure PC-PGI > Makefile # make Where I have removed the references to '-byteswapio' and '-Msecond_underscore', the make process completes with pgf77-Warning-Unknown switch: -pc64 and gives me a cpmd.x executable which runs the test cases just fine. However, when I compile using: # ./Configure PC-PGI-MPI > Makefile # make I get the following output: rm -f cpmd.f /lib/cpp -P -C -traditional -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT -DPARALLEL -DMP_LIBRARY=__MPI -DMYRINET ./cpmd.F ./cpmd.f mpif77 -c -fast -Mr8 -pc64 -Msignextend ./cpmd.f -o ./cpmd.o f77: unrecognized option `-pc64' f771: Unrecognized option `-fast' In file included from ./cpmd.f:11: system.h: In subroutine `cpmd': system.h:76: POINTER (IP_NKPBL,NKPBL),(IP_KPBEG,KPBEG) 1 2 Unrecognized statement name at (1) and invalid form for assignment or statement-function definition at (2) system.h:183: POINTER (IP_MAPGP,MAPGP) 1 2 Unrecognized statement name at (1) and invalid form for assignment or statement-function definition at (2) system.h:195: POINTER(IP_IATPT,IATPT),(IP_IPEPT,IPEPT),(IP_IATPE,IATPE) 1 2 Unrecognized statement name at (1) and invalid form for assignment or statement-function definition at (2) system.h:473: POINTER (IP_NASSEL,NASSEL) 1 2 Unrecognized statement name at (1) and invalid form for assignment or statement-function definition at (2) In file included from ./cpmd.f:13: prop.inc:52: POINTER (IP_ICUBEORB,ICUBEORB),(IP_Z_11,Z_11) 1 2 Unrecognized statement name at (1) and invalid form for assignment or statement-function definition at (2) system.h:77: COMMON/NKIP/ IP_NKPBL,IP_KPBEG 1 How do I fix this? Thanks. Jim From piana at inorg.chem.ethz.ch Mon Aug 11 03:40:15 2003 From: piana at inorg.chem.ethz.ch (Stefano Piana) Date: Mon, 11 Aug 2003 09:40:15 +0800 Subject: [CPMD-list] Cell optimization with UPP Message-ID: <3F36F3FF.7060609@inorg.chem.ethz.ch> Hallo! I would like to optimize a cell using Vanderbilt Ultrasoft Pseudopotentials with CPMD 3.7. Unfortunately, after optimizing the wavefunction, the program coredump after the routine DQVAN2. These are the last lines of the output. 14 6.495E-05 7.878E-06 -88.029086 -2.614E-06 1.51 15 3.668E-05 4.768E-06 -88.029087 -6.344E-07 1.51 16 2.412E-05 2.967E-06 -88.029087 -1.649E-07 1.50 *** STRESS| THE NEW SIZE OF THE PROGRAM IS 24708 kBYTES *** *** DQVAN2| THE NEW SIZE OF THE PROGRAM IS 28492 I am running CPMD compiled with the PGF90 on a linux PC. If I remove from the imput file the line STEEPEST DESCENT CELL, the geometry optimization proceeds to convergency. If I use Martins-Troullier pseudopotentials with the same input file the cell optimization proceeds without apparent problems. Thus, it seems that the problem emerges only when I combine UPP with cell optimization. Any suggestion? Stefano From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Tue Aug 12 13:13:45 2003 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Tue, 12 Aug 2003 13:13:45 +0200 Subject: [CPMD-list] MPI and SMP on P4 Linux using PGI compilers In-Reply-To: Your message of "Sat, 09 Aug 2003 23:20:42 -0000." <200308092320.43048.cpmd@kressworks.com> Message-ID: <200308121113.h7CBDjm04483@yello.theochem.ruhr-uni-bochum.de> >>> "JK" == cpmd writes: JK> When I do JK> # Configure JK> to get a list of target platforms, I see JK> PC-PGI PC-PGI-MPI JK> PC-PGI-MPI-QMMM PC-PGI-QMMM JK> PC-IFC-MPI PC-IFC JK> and JK> IBM-SP3 IBM-SP3-SMP JK> IBM-SP4 IBM-SP4-SMP JK> IBM-SP4-64 IBM-SP4-SMP-64 JK> but no SMP for PC-PGI. Is SMP supported on Linux PCs using Reh Hat 7.3 and JK> PGI compilers? How about PC-PGI-MPI-SMP? hi jim, smp configurations are supported by using openmp directives. i have been (so far) successfully able to compile and test such a binary with the PGI compiler (just add the flag -mp). with the intel compiler you should use the flag -openmp. so much for the good news. now the bad news: it does not improve the performance on any pc hardware i could get my hands on so far. to explain: the OpenMP parallelization is not as complete as the MPI parallelization. so for a small number of nodes, you are almost always better off using MPI parallelization over a combination of shared memory and TCP/IP (lam-mpi, for example, does this pretty efficiently). as far as i understand it, cpmd does the mpi distributed memory parallization by distributing the g-space over the mpi-nodes. there is a scalability limit to this. sooner or later the amount of work is distributed so unevenly over the nodes, that the time they have to wait for the slowest node to finish, takes longer that the time you win by adding nodes. this is the regime where the openmp parallelization is supposed to kick in. unfortunately, with current pc hardware this does not seem to be true. when you compile for openmp you will lose one register and there also is some overhead in spawning threads etc. in my tests, this seems to completely eat up the speedup of the openmp parallization. in fact it was faster to use only one (of the two cpus) on each node. you also have to keep in mind that pc hardware is so memory bandwidth starved, that using the second cpu significantly slows down the fist cpu (just run two single cpu jobs simultaneously and compare the timing to a single cpu job when leaving the second cpu idle). in my tests i got on dual athlon machines with AMD-760MPX chipset and PC266-DDR-ECC memory about 160% computing power of a single cpu machine when running two jobs simulatneously. on a dual pentium 4 machine things get even worse. on a intel e7500 dual channel(!) PC200-DDR memory board i got about 120% the computing power when using the second cpu. in fact, when i activated openmp/multithreading the job got slower compared to the single cpu job. the penalty seems a little smaller, when a ran _really_ small jobs. to summarize, if you want to get the most out of your smp-pcs, try the following: - if you have a limited number of smp-nodes (say less than 32-48 cpus, depending on the size of the system and the cutoff), you should use mpi parallelization only. - if you have more nodes available, try using them in single cpu mode first and compare to the full-mpi/openmp-mpi speed. - try to vary the number of nodes. due to the distributed memory parallelization strategy, there are 'magic numbers' that may vary from system to system and with the cutoff where you get a very good load distribution and thus a good overall performace. hope this helps, axel. JK> Thanks. JK> Jim Kress JK> _______________________________________________ JK> CPMD-list mailing list JK> CPMD-list at cpmd.org JK> http://www.cpmd.org/mailman/listinfo/cpmd-list -- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Tue Aug 12 13:17:26 2003 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Tue, 12 Aug 2003 13:17:26 +0200 Subject: [CPMD-list] Cell optimization with UPP In-Reply-To: Your message of "Mon, 11 Aug 2003 09:40:15 +0800." <3F36F3FF.7060609@inorg.chem.ethz.ch> Message-ID: <200308121117.h7CBHQv04665@yello.theochem.ruhr-uni-bochum.de> >>> "SP" == Stefano Piana writes: SP> Hallo! SP> I would like to optimize a cell using Vanderbilt Ultrasoft SP> Pseudopotentials with CPMD 3.7. Unfortunately, after optimizing the SP> wavefunction, the program coredump after the routine DQVAN2. These are SP> the last lines of the output. SP> 14 6.495E-05 7.878E-06 -88.029086 -2.614E-06 1.51 SP> 15 3.668E-05 4.768E-06 -88.029087 -6.344E-07 1.51 SP> 16 2.412E-05 2.967E-06 -88.029087 -1.649E-07 1.50 SP> *** STRESS| THE NEW SIZE OF THE PROGRAM IS 24708 kBYTES *** SP> *** DQVAN2| THE NEW SIZE OF THE PROGRAM IS 28492 SP> I am running CPMD compiled with the PGF90 on a linux PC. If I remove SP> from the imput file the line STEEPEST DESCENT CELL, the geometry SP> optimization proceeds to convergency. SP> If I use Martins-Troullier pseudopotentials with the same input file the SP> cell optimization proceeds without apparent problems. SP> Thus, it seems that the problem emerges only when I combine UPP with SP> cell optimization. SP> Any suggestion? did you try the latest version (3.7.2)? iirc, there were some memory management bugfixes related to vanderbilt uspps. axel. SP> Stefano SP> _______________________________________________ SP> CPMD-list mailing list SP> CPMD-list at cpmd.org SP> http://www.cpmd.org/mailman/listinfo/cpmd-list -- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From kwoods at stanford.edu Tue Aug 12 18:41:22 2003 From: kwoods at stanford.edu (Kristina Woods) Date: Tue, 12 Aug 2003 09:41:22 -0700 Subject: [CPMD-list] unknown keywords? Message-ID: <000801c360f0$90cb5c90$36ae0c80@Redwoods> Hello, I have just started using cpmd. I have been able to do the single test run that we have on our computer. But when I try my own using my own input file, I get errors from 'unkown keywords'. Why would this happen? I'm sure I'm doing something wrong, but I really don't know what it is. Thank you, Kristina :) Here is the input file and the subsequent error: &CPMD OPTIMIZE WAVEFUNCTION STRUCTURE BONDS ANGLES RESTART WAVEFUNCTION COORDINATES FILEPATH /u/ac/kwoods/waterdata &END &SYSTEM ANGSTROM SYMMETRY 1 CELL 9.65 1.0 1.0 0 0 0 CUTOFF 70.0 POINT GROUP AUTO &END *********************************************************************************************************************************************************************************************************************************************** THE INPUT FILE IS: 32water.inp THIS JOB RUNS ON: Cu12 THE CURRENT DIRECTORY IS: /u/ac/kwoods/waterdata THE TEMPORARY DIRECTORY IS: /u/ac/kwoods/waterdata THE PROCESS ID IS: 2908302 THE JOB WAS SUBMITTED BY: kwoods SINGLE POINT DENSITY OPTIMIZATION PATH TO THE RESTART FILES: &END^M/ RESTART WITH OLD ORBITALS RESTART WITH OLD ION POSITIONS GRAM-SCHMIDT ORTHOGONALIZATION MAXIMUM NUMBER OF STEPS: 10000 STEPS PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS STORE INTERMEDIATE RESULTS EVERY 10001 STEPS NUMBER OF DISTINCT RESTART FILES: 1 TEMPERATURE IS CALCULATED ASSUMING EXTENDED BULK BEHAVIOR FICTITIOUS ELECTRON MASS: 400.0000 TIME STEP FOR ELECTRONS: 5.0000 TIME STEP FOR IONS: 5.0000 CONVERGENCE CRITERIA FOR WAVEFUNCTION OPTIMIZATION: 1.0000E-05 WAVEFUNCTION OPTIMIZATION BY PRECONDITIONED DIIS THRESHOLD FOR THE WF-HESSIAN IS .5000 MAXIMUM NUMBER OF VECTORS RETAINED FOR DIIS: 10 STEPS UNTIL DIIS RESET ON POOR PROGRESS: 10 FULL ELECTRONIC GRADIENT IS USED SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS NUMBER OF SPLINE POINTS: 5000 ================================================================ = UNKNOWN KEYWORDS = = ^M = = &SYSTEM^M = = ANGSTROM^M = = = = SYMMETRY^M = = 1^M = = CELL^M = = = = 9.65 1.0 1.0 0 0 0^M = = CUTOFF^M = = 70.0^M = ================================================================ EXCHANGE CORRELATION FUNCTIONALS LDA EXCHANGE: SLATER (ALPHA = .66667) LDA CORRELATION: LEE, YANG & PARR [C.L. LEE, W. YANG, AND R.G. PARR, PRB 37 785 (1988)] GRADIENT CORRECTED FUNCTIONAL DENSITY THRESHOLD: 1.00000E-08 EXCHANGE ENERGY [A.D. BECKE, PHYS. REV. A 38, 3098 (1988)] PARAMETER BETA: .004200 CORRELATION ENERGY [J.P. PERDEW, PHYS. REV. B 33, 8822 (1986)] ERROR READING THE SYMMETRY NUMBER SYSIN: ERROR IN READING INPUT FILE -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20030812/e07f5263/attachment.html From Ari.P.Seitsonen at iki.fi Thu Aug 14 10:20:53 2003 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Thu, 14 Aug 2003 10:20:53 +0200 Subject: [CPMD-list] unknown keywords? In-Reply-To: <000801c360f0$90cb5c90$36ae0c80@Redwoods> (kwoods@stanford.edu) References: <000801c360f0$90cb5c90$36ae0c80@Redwoods> Message-ID: <200308140820.h7E8Kra17694@magadino.cscs.ch> Dear Kristina, > &CPMD > OPTIMIZE WAVEFUNCTION > STRUCTURE BONDS ANGLES > RESTART WAVEFUNCTION COORDINATES > FILEPATH /u/ac/kwoods/waterdata > &END > > &SYSTEM > ANGSTROM > SYMMETRY > 1 > CELL > 9.65 1.0 1.0 0 0 0 > CUTOFF > 70.0 > POINT GROUP > AUTO > &END You should provide the argument for 'FILEPATH' on the following, not the same line as the keyword. Now "&END" is understood as the path to the files, thus the end of the section '&CPMD' is no found in time. Greetings from Zurich with thunderstorm, apsi -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland From hutter at pci.unizh.ch Thu Aug 14 10:47:38 2003 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Thu, 14 Aug 2003 10:47:38 +0200 (MEST) Subject: [CPMD-list] unknown keywords? In-Reply-To: <000801c360f0$90cb5c90$36ae0c80@Redwoods> References: <000801c360f0$90cb5c90$36ae0c80@Redwoods> Message-ID: Hi try FILEPATH /u/ac/kwoods/waterdata instead of FILEPATH /u/ac/kwoods/waterdata Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Tue, 12 Aug 2003, Kristina Woods wrote: > Hello, > > I have just started using cpmd. I have been able to do the single test run that we have on our computer. But when I try my own using my own input file, I get errors from 'unkown keywords'. Why would this happen? I'm sure I'm doing something wrong, but I really don't know what it is. > > Thank you, > > Kristina :) > > Here is the input file and the subsequent error: > > &CPMD > OPTIMIZE WAVEFUNCTION > STRUCTURE BONDS ANGLES > RESTART WAVEFUNCTION COORDINATES > FILEPATH /u/ac/kwoods/waterdata > &END > > &SYSTEM > ANGSTROM > SYMMETRY > 1 > CELL > 9.65 1.0 1.0 0 0 0 > CUTOFF > 70.0 > POINT GROUP > AUTO > &END > > *********************************************************************************************************************************************************************************************************************************************** > > THE INPUT FILE IS: 32water.inp > THIS JOB RUNS ON: Cu12 > THE CURRENT DIRECTORY IS: > /u/ac/kwoods/waterdata > THE TEMPORARY DIRECTORY IS: > /u/ac/kwoods/waterdata > THE PROCESS ID IS: 2908302 > THE JOB WAS SUBMITTED BY: kwoods > > > SINGLE POINT DENSITY OPTIMIZATION > > PATH TO THE RESTART FILES: &END^M/ > RESTART WITH OLD ORBITALS > RESTART WITH OLD ION POSITIONS > GRAM-SCHMIDT ORTHOGONALIZATION > MAXIMUM NUMBER OF STEPS: 10000 STEPS > PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS > STORE INTERMEDIATE RESULTS EVERY 10001 STEPS > NUMBER OF DISTINCT RESTART FILES: 1 > TEMPERATURE IS CALCULATED ASSUMING EXTENDED BULK BEHAVIOR > FICTITIOUS ELECTRON MASS: 400.0000 > TIME STEP FOR ELECTRONS: 5.0000 > TIME STEP FOR IONS: 5.0000 > CONVERGENCE CRITERIA FOR WAVEFUNCTION OPTIMIZATION: 1.0000E-05 > WAVEFUNCTION OPTIMIZATION BY PRECONDITIONED DIIS > THRESHOLD FOR THE WF-HESSIAN IS .5000 > MAXIMUM NUMBER OF VECTORS RETAINED FOR DIIS: 10 > STEPS UNTIL DIIS RESET ON POOR PROGRESS: 10 > FULL ELECTRONIC GRADIENT IS USED > SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS > NUMBER OF SPLINE POINTS: 5000 > > ================================================================ > = UNKNOWN KEYWORDS = > = ^M = > = &SYSTEM^M = > = ANGSTROM^M = > = = > = SYMMETRY^M = > = 1^M = > = CELL^M = > = = > = 9.65 1.0 1.0 0 0 0^M = > = CUTOFF^M = > = 70.0^M = > ================================================================ > > > EXCHANGE CORRELATION FUNCTIONALS > LDA EXCHANGE: SLATER (ALPHA = .66667) > LDA CORRELATION: LEE, YANG & PARR > [C.L. LEE, W. YANG, AND R.G. PARR, PRB 37 785 (1988)] > GRADIENT CORRECTED FUNCTIONAL > DENSITY THRESHOLD: 1.00000E-08 > EXCHANGE ENERGY > [A.D. BECKE, PHYS. REV. A 38, 3098 (1988)] > PARAMETER BETA: .004200 > CORRELATION ENERGY > [J.P. PERDEW, PHYS. REV. B 33, 8822 (1986)] > > ERROR READING THE SYMMETRY NUMBER > SYSIN: ERROR IN READING INPUT FILE From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Thu Aug 14 11:16:08 2003 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Thu, 14 Aug 2003 11:16:08 +0200 (CEST) Subject: [CPMD-list] unknown keywords? In-Reply-To: <000801c360f0$90cb5c90$36ae0c80@Redwoods> Message-ID: On Tue, 12 Aug 2003, Kristina Woods wrote: KW> Hello, KW> KW> I have just started using cpmd. I have been able to do the single test run that we have on our computer. But when I try my own using my own input file, I get errors from 'unkown keywords'. Why would this happen? I'm sure I'm doing something wrong, but I really don't know what it is. KW> KW> Thank you, KW> KW> Kristina :) KW> KW> Here is the input file and the subsequent error: [...] KW> ================================================================ KW> = UNKNOWN KEYWORDS = KW> = ^M = KW> = &SYSTEM^M = KW> = ANGSTROM^M = KW> = = KW> = SYMMETRY^M = KW> = 1^M = KW> = CELL^M = KW> = = KW> = 9.65 1.0 1.0 0 0 0^M = KW> = CUTOFF^M = KW> = 70.0^M = KW> ================================================================ dear kristina, the error lies in the ^M (control-m) characters. it seems you have somehow transferred you input file from a DOS/Windows machine to a unix machine in binary and not in text mode. dos/windows and unix have different codes to signal the end of a line of text (i.e. dos/windows add the ^M) there are several ways of removing the control-m characters from your input file. the most portable one is probably: tr -d '\015' < input.old > input.new more convenient are tools like dos2unix/unix2dos or tofrodos (). take care, axel. -- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.rub.de ======================================================================= From ct at chemie.hu-berlin.de Thu Aug 14 14:37:33 2003 From: ct at chemie.hu-berlin.de (Christian Tuma) Date: Thu, 14 Aug 2003 14:37:33 +0200 Subject: [CPMD-list] unknown keywords? In-Reply-To: <000801c360f0$90cb5c90$36ae0c80@Redwoods> References: <000801c360f0$90cb5c90$36ae0c80@Redwoods> Message-ID: <20030814123733.GB20884@uranus.chemie.hu-berlin.de> Hi, your input file seems to be created under a non-UNIX-like operating system in contrast to where the CPMD job runs under. That's why special characters (^M) appear at the end of every line in your input which confuse CPMD. Simply edit your input on a UNIX-like machine, make sure that these special characters get removed. Good luck, Christian. > PATH TO THE RESTART FILES: &END^M/ > ... > ================================================================ > = UNKNOWN KEYWORDS = > = ^M = > = &SYSTEM^M = > = ANGSTROM^M = > = = > = SYMMETRY^M = > = 1^M = > = CELL^M = > = = > = 9.65 1.0 1.0 0 0 0^M = > = CUTOFF^M = > = 70.0^M = > ================================================================ -- Christian Tuma Humboldt-Universitaet Berlin ct at chemie.hu-berlin.de Arbeitsgruppe Quantenchemie (Prof. Sauer) phone: +49-30-20937140 Brook-Taylor-Str. 2, 12489 Berlin, GERMANY fax: +49-30-20937136 http://www.chemie.hu-berlin.de/ag_sauer From reply at WindowFlower.com Thu Aug 14 18:25:12 2003 From: reply at WindowFlower.com (Window Flower) Date: Fri, 15 Aug 2003 00:25:12 +0800 Subject: [CPMD-list] The Magic of Artistic Paper-Cuts Message-ID: <200308141623.SAA11014@internet-fence.zurich.ihost.com> An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20030815/0a9bd160/attachment.html From tironem at fiu.edu Thu Aug 14 21:59:25 2003 From: tironem at fiu.edu (Massimiliano Tirone) Date: Thu, 14 Aug 2003 15:59:25 -0400 (EDT) Subject: [CPMD-list] problems using correlation functional Message-ID: Hi, I am experiencing problems using correlation functional. When I create and input file with something like: &DFT FUNCTIONAL LDA LDA CORRELATION PZ &END I have a crash with an ** Address Error ** If I remove LDA CORRELATION PZ, using just: &DFT FUNCTIONAL LDA &END the run is ok but in the output file there is something like: LDA EXCHANGE: NONE LDA XC THROUGH PADE APPROXIMATION S.GOEDECKER, J.HUTTER, M.TETER PRB 54 1703 (1996) My patch for this is to replace FUNCTIONAL LDA with: &DFT SLATER 0.6666666 LDA FUNCTIONAL NO &END and in the output I get: EXCHANGE CORRELATION FUNCTIONALS LDA EXCHANGE: SLATER (ALPHA = 0.66667) LDA CORRELATION: NONE now, the only way I can have exchange and correlation functionals is to use in the input file: &DFT SLATER 0.66666666 LDA CORRELATION PZ EXCHANGE CORRELATION TABLE NO &END and in the output file everything seems fine: EXCHANGE CORRELATION FUNCTIONALS LDA EXCHANGE: SLATER (ALPHA = 0.66667) LDA CORRELATION: PERDEW & ZUNGER [J.P. PERDEW AND A ZUNGER, PRB 23 5048 (1981)] Does this make any sense? Last piece of information, this is independent from: type of atoms, type of correlation functionals, type of system (crystal or molecule) and type of PP (KB or Goedecker but I havent tried Vanderbilt PP). CPMD (3.7.1) is compiled with IFC and is running on a P4 machine. Max ps. hope this is not too confusing. From iivanov at cmm.chem.upenn.edu Sat Aug 16 05:15:19 2003 From: iivanov at cmm.chem.upenn.edu (Ivaylo Ivanov) Date: Fri, 15 Aug 2003 23:15:19 -0400 Subject: [CPMD-list] uspp problem Message-ID: <1061003719.3f3da1c7ac2cf@webmail.sas.upenn.edu> Hello all, I'm having a problem using CPMD 3.7.2 with ultrasoft pseudopotentials on the Compaq Alpha server (lemieux) at the Pittsburgh Supercomputing center. The same input runs with no apparent difficulties using Troullier-Martins PPs or with USPPs on an IBM SP platform. If anyone has had experience running on the same architecture and knows about this problem, please let me know how to resolve it. Any input would be greatly appreciated.Thank you. Sincerely, Ivaylo Ivanov Here is an exerpt from the input file: &CPMD OPTIMIZE WAVEFUNCTION PCG MINIMIZE UNIT HESSIAN mOLECULAR dYNAMICS rESTART cOORDINATES vELOCITIES wAVEFUNCTION lATEST LSD TIMESTEP 5.0 MAXSTEP 2600 STORE 200 EMASS 800.D0 TEMPERATURE 300 NOSE IONS 300. 500 TRAJECTORY SAMPLE 5 RESTFILE 2 &DFT FUNCTIONAL BP GC-CUTOFF 1.0E-05 &END &SYSTEM SYMMETRY 8 CELL 25.5 1.0 0.85 0. 0. 0. CUTOFF 28.0 CHARGE 0. MULTIPLICITY 11. &END &ATOMS *O_VDB_BP.uspp NEWF BINARY LMAX=P LOC=P .............. *H_VDB_BP.uspp NEWF BINARY LMAX=S .............. *C_VDB_BP.uspp NEWF BINARY LMAX=P LOC=P .......... *N_VDB_BP.uspp NEWF BINARY LMAX=P LOC=P .............. *Mn_VDB_BP.uspp NEWF BINARY LMAX=D LOC=D .............. ISOTOPE 15.9994 2.01410 12.01115 14.0067 54.93800 CONSTRAINTS FIX ATOMS 9 150 164 170 156 161 152 147 169 144 FIX STRUCTURE 1 DIST 174 7 -999 END CONSTRAINTS &END Here is the output: ............. NFI GEMAX CNORM ETOT DETOT TCPU 1 4.957E-01 9.505E-03 -990.293725 0.000E+00 27.86 LINE SEARCH : LAMBDA=.169 ENERGY = -1032.9356 2 4.952E-01 9.506E-03 -990.807894 -5.142E-01 31.88 LINE SEARCH : LAMBDA=.237 ENERGY = -1074.2195 3 6.153E-01 7.977E-03 -1032.080818 -4.127E+01 33.02 LINE SEARCH : LAMBDA=.248 ENERGY = -1094.9185 4 3.028E-01 4.850E-03 -1077.159149 -4.508E+01 29.16 LINE SEARCH : LAMBDA=.384 ENERGY = -1102.6279 5 2.180E-01 2.868E-03 -1094.857543 -1.770E+01 27.13 LINE SEARCH : LAMBDA=.582 ENERGY = -1109.3259 6 4.833E-02 2.492E-03 -1102.646254 -7.789E+00 106.75 LINE SEARCH : LAMBDA=.599 ENERGY = -1112.6360 7 2.741E-02 2.053E-03 -1109.331357 -6.685E+00 29.26 LINE SEARCH : LAMBDA=.691 ENERGY = -1114.4586 8 2.429E-02 1.161E-03 -1112.597411 -3.266E+00 23.27 LINE SEARCH : LAMBDA=.447 ENERGY = -1115.3939 9 1.586E-02 9.121E-04 -1114.447950 -1.851E+00 26.32 LINE SEARCH : LAMBDA=.411 ENERGY = -1116.0871 10 1.691E-02 7.629E-04 -1115.452530 -1.005E+00 24.97 LINE SEARCH : LAMBDA=.469 ENERGY = -1116.8200 11 1.418E-02 8.122E-04 -1116.143979 -6.914E-01 26.06 LINE SEARCH : LAMBDA=.510 ENERGY = -1117.3461 12 1.392E-02 5.740E-04 -1116.846097 -7.021E-01 23.72 LINE SEARCH : LAMBDA=.434 ENERGY = -1117.7142 13 1.640E-02 5.112E-04 -1117.356211 -5.101E-01 23.17 LINE SEARCH : LAMBDA=.455 ENERGY = -1118.0642 14 1.200E-02 4.792E-04 -1117.733713 -3.775E-01 24.24 prun: /scratch2/6/ivanov/ARG/ARG_fep/rla_h2o_box_uspp/cpmd.x (pid 639644) killed by signal 6 prun: generating backtrace for /scratch2/6/ivanov/ARG/ARG_fep/rla_h2o_box_uspp/c pmd.x /local/core/rms/499817/core.cpmd.x.iam64.0 Welcome to the Ladebug Debugger Version 68 (built Sep 16 2002 for Tru64 UNIX) ------------------ object file name: /scratch2/6/ivanov/ARG/ARG_fep/rla_h2o_box_uspp/cpmd.x core file name: /local/core/rms/499817/core.cpmd.x.iam64.0 Reading symbolic information ...done Core file produced from executable 'cpmd.x' forrtl: severe (174): SIGSEGV, segmentation fault occurred -- Ivaylo Ivanov Center for Molecular Modeling University of Pennsylvania, Tel: (215)573 8697 231 S. 34th St. Fax: (215)573 6233 Philadelphia, PA 19104 E-mail:iivanov at cmm.chem.upenn.edu From rjsa at mail.shcnc.ac.cn Mon Aug 18 13:26:03 2003 From: rjsa at mail.shcnc.ac.cn (Rongjian Sa) Date: Mon, 18 Aug 2003 19:26:3 +0800 Subject: [CPMD-list] How to modify results more reasonable? Message-ID: <20030818112435.B32482085FC@mail.shcnc.ac.cn> Dear CPMD users, I want to computer the binding energy of ammonium-benzene complex. It is well know this complex contains three stable structures (we denote them as 1, 2 and 3, 1 means one hydrogen atom of ammonium toward benzene, 2 means two hydrogen atoms of ammonium toward benzene, 3 means three hydrogen atoms of ammonium toward benzene). Previous B3LYP and MP2 calculation using large basis sets shown 2 is most stable and CPMD/70Ry calculation also proven this. The calculated binding energy of 2 is also similar. But for 1 and 3, CPMD and Gaussian program give different results. In B3LYP and MP2 calculation, 3 is more stable than 1. While in CPMD calculation, 1 is more stable than 3. Also in CPMD calculation, with the increasing of cell size, the deviation from experimental results increasing. I have tried to increasing the convergence of optimization. But it seems little effect. I wonder if you can give me some advice about my calculation. Input file of 1: &CPMD RESTART WAVEFUNCTION LATEST OPTIMIZE GEOMETRY CONVERGENCE 1.D-5 5.D-5 EMASS 500 MIRROR &END &SYSTEM SYMMETRY 1 CELL 15.1178 1.0 1.0 0 0 0 CUTOFF 70.0 CHARGE 1 &END &ATOMS *C_MT_GIA_BLYP KLEINMAN-BYLANDER LMAX=P 6 0.0023 2.6441 -1.2327 2.2960 1.3201 -1.2362 2.2955 -1.3326 -1.2336 0.0009 -2.6548 -1.2281 -2.2930 -1.3312 -1.2271 -2.2922 1.3216 -1.2297 *N_MT_GIA_BLYP KLEINMAN-BYLANDER LMAX=P 1 -0.0069 0.0238 4.7434 *H_MT_BLYP KLEINMAN-BYLANDER LMAX=S 10 0.0032 4.7040 -1.2833 4.0772 2.3470 -1.2920 4.0760 -2.3608 -1.2869 0.0004 -4.7150 -1.2769 -4.0740 -2.3586 -1.2757 -4.0728 2.3496 -1.2809 -0.0029 -0.0039 2.7647 -1.6017 0.9524 5.3801 1.5842 0.9530 5.3884 -0.0085 -1.8058 5.4252 &END &DFT NEWCODE FUNCTIONAL BLYP &END Input file for 2: &ATOMS *C_MT_GIA_BLYP KLEINMAN-BYLANDER LMAX=P 6 0.0001 2.6507 -1.1977 -0.0005 -2.6471 -1.1761 -2.2965 1.3281 -1.1968 2.2964 1.3277 -1.1951 2.2963 -1.3242 -1.1845 -2.2970 -1.3237 -1.1861 *N_MT_GIA_BLYP KLEINMAN-BYLANDER LMAX=P 1 0.0008 -0.0084 4.6011 *H_MT_BLYP KLEINMAN-BYLANDER LMAX=S 10 0.0003 4.7116 -1.2507 -0.0006 -4.7083 -1.2129 -4.0767 2.3580 -1.2364 4.0768 2.3573 -1.2334 4.0767 -2.3541 -1.2144 -4.0774 -2.3534 -1.2175 -0.0017 1.5778 3.4438 0.0049 -1.5530 3.3854 -1.5944 -0.0313 5.7201 1.5946 -0.0247 5.7222 &END Input file for 3: *C_MT_GIA_BLYP KLEINMAN-BYLANDER LMAX=P 6 0.0000 1.2865 2.6672 2.2953 1.2470 1.3452 2.2956 1.1696 -1.3075 0.0000 1.1273 -2.6313 -2.2956 1.1696 -1.3075 -2.2953 1.2470 1.3452 *N_MT_GIA_BLYP KLEINMAN-BYLANDER LMAX=P 1 0.0000 -4.6951 -0.0804 *H_MT_BLYP KLEINMAN-BYLANDER LMAX=S 10 0.0000 1.4037 4.7256 4.0760 1.3412 2.3727 4.0774 1.1969 -2.3365 0.0000 1.1327 -4.6935 -4.0774 1.1969 -2.3365 -4.0760 1.3412 2.3727 0.0000 -6.6392 -0.2002 -1.5821 -4.0530 0.8709 1.5821 -4.0530 0.8709 0.0000 -3.8717 -1.8560 &END -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20030818/beb446af/attachment.html From aldo at titan.ipicyt.edu.mx Mon Aug 18 19:31:07 2003 From: aldo at titan.ipicyt.edu.mx (DR.ALDO ROMERO) Date: Mon, 18 Aug 2003 12:31:07 -0500 (CDT) Subject: [CPMD-list] Kohn-Sham states Message-ID: Dear CPMD'users, I am having some troubles in getting the KS states converged. After a succesful geometry optimization, I have tried to calculate the Kohn-Sham states by using: &CPMD KOHN-SHAM ENERGIES 0 RESTART WAVEFUNCTION COORDINATES LATEST &END but after the default number of iterations, most of my KS energies are not converged (NC at the end of the value). this is strange because I am not increasing my space, I am using the same number of states I have used for the optimization. Any advice on this issue would be appreciated! Thanks -aldo. ------------------------------------------------------------------------- Prof. Aldo Humberto Romero IPICyT Camino a la presa San Jose 2055 Colonia Lomas 4a seccion C.P 78216 San Luis Potosi, SLP Mexico email: aldo at ipicyt.edu.mx Phone: (52)-444-8342000 Ext 2038 Fax: (52)-444-8342010 http://materials.ipicyt.edu.mx/ From jimkress at kressworks.com Tue Aug 19 02:14:48 2003 From: jimkress at kressworks.com (Jim Kress) Date: Tue, 19 Aug 2003 00:14:48 +0000 Subject: [CPMD-list] OpenMP Parallelization of CPMD Message-ID: <200308190014.48668.jimkress@kressworks.com> I have managed to get CPMD 3.7.2 running in parallel using MPI (MPICH) and the Portland Group Compilers (Thanks Axel!). I'd like to try to get it to run in parallel with OpenMP to compare performance with MPI (MPICH). The CPMD documentation alludes to OpenMP but gives no directions on how to do the necessary compiles. Also, Configure has no (obvious) information on how to create an OpenMP parallel version of CPMD. Anybody know how to do this and is willing to share with the list? Thanks. Jim From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Tue Aug 19 07:51:04 2003 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Tue, 19 Aug 2003 07:51:04 +0200 Subject: [CPMD-list] Re: OpenMP Parallelization of CPMD In-Reply-To: Your message of "Tue, 19 Aug 2003 00:14:48 -0000." <200308190014.48668.jimkress@kressworks.com> Message-ID: <200308190551.h7J5p4C19162@yello.theochem.ruhr-uni-bochum.de> >>> "JK" == Jim Kress writes: JK> I have managed to get CPMD 3.7.2 running in parallel using MPI (MPICH) and the JK> Portland Group Compilers (Thanks Axel!). I'd like to try to get it to run in JK> parallel with OpenMP to compare performance with MPI (MPICH). JK> The CPMD documentation alludes to OpenMP but gives no directions on how to do JK> the necessary compiles. Also, Configure has no (obvious) information on how JK> to create an OpenMP parallel version of CPMD. JK> Anybody know how to do this and is willing to share with the list? hi jim. to compile for OpenMP you only need to signal the compiler to look for OpenMP directives. with the portland compilers this is done by adding the flag '-mp' to the FC and LD makefile variables, e.g.: CC = gcc -O2 -Wall -D_REENTRANT FC = pgf77 -c -fast -mp -tp athlon -D_REENTRANT LD = pgf77 -fast -mp -tp athlon -D_REENTRANT then recompile everything (make clean ; make) if you want to enable OpenMP during a parallel run, you have to set the environment variable OMP_NUM_THREADS to the number of cpus, you want to use for OpenMP (usually 2 on SMP PCs). so you have to type: OMP_NUM_THREADS=2 export OMP_NUM_THREADS if you have a bourne shell and setenv OMP_NUM_THREADS 2 if you have a c-shell. you then start the cpmd job and should see multiple cpmd threads/processes instead of a single one. the tricky part is to make that work on a parallel run. please refer to your MPICH documentation on how to export environment variables to 'remote' nodes. be prepared for depressing results. although a combination of MPI and OpenMP seems to be a smart choice, if you want to run a cpmd job on a large number of cpus (particularly if you do not have a high-speed interconnect) , i have not found any improvement on PC hardware. in fact, i was usually better off using either only MPI or not using the second CPU at all (the latter especially on dual pentium-4 machines). good luck, axel. p.s.: if you find the time, please let me know of your findings. TIA, a. JK> Thanks. JK> Jim -- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From stubbs at chemsun.chem.umn.edu Wed Aug 20 00:03:52 2003 From: stubbs at chemsun.chem.umn.edu (John Stubbs) Date: Tue, 19 Aug 2003 17:03:52 -0500 (CDT) Subject: [CPMD-list] Incorrect usage of FINITE DIFFERENCES keyword? In-Reply-To: <200308190014.48668.jimkress@kressworks.com> Message-ID: <20030819170004.W57754-100000@chemsun.chem.umn.edu> Hello all, I was wondering if anyone could see my mistake in input: I only wish to calculate the frequency of a particular atom, and using CPMD version 3.7.1 according to the manual I should be able to specify a COORD=x and RADIUS=y value on the same line as the finite differences step size. However, the program stops upon reading that line: PROGRAM CPMD STARTED AT: Tue Aug 19 23:59:50 2003 CONTROL| ERROR IN READING INPUT FILE THE LAST TWO LINES READ WERE FINITE 0.01 PROGRAM STOPS IN SUBROUTINE CONTROL| 999 Produced from the input file &CPMD VIBRATIONAL ANALYSIS FD FINITE DIFFERENCES 0.01 COORD=1 RADIUS=1.0 RESTART WAVEFUNCTION COORDINATES VELOCITIES LATEST &END &DFT FUNCTIONAL BLYP &END &SYSTEM SYMMETRY 0 CELL 10.000 1.0 1.0 0 0 0 CUTOFF 50.0 &END &ATOMS *O_BLYP.PP30 KLEINMAN-BYLANDER LMAX=P 1 4.8636 5.1640 4.9149 *H_BLYP.PP30 LMAX=S 2 5.4007 3.5914 4.1224 5.6902 5.0964 6.5586 ISOTOPE 16.d0 2.d0 &END Thanks in advance! John Stubbs From jimkress at kressworks.com Wed Aug 20 22:38:47 2003 From: jimkress at kressworks.com (Jim Kress) Date: Wed, 20 Aug 2003 20:38:47 +0000 Subject: Fwd: Re: [CPMD-list] OpenMP Parallelization of CPMD Message-ID: <200308202038.47321.jimkress@kressworks.com> Here is a copy of the email I sent to Pierre in response to his question about CPMD MPI with PGI. It may be of some use to others who are trying to do this compile. Jim ---------- Forwarded Message ---------- Subject: Re: [CPMD-list] OpenMP Parallelization of CPMD Date: Wed, 20 Aug 2003 20:35:45 +0000 From: Jim Kress To: Pierre Moth? Esteves Dear Pierre, The secret to compiling CPMD with MPI (MPICH) using the Portland Group compilers is to make sure you have compiled your MPI code with the same set of compilers. In my case, the MPI code was MPICH. To configure MPICH with pgi: # su -l root # cd /opt # mv mpich-1.2.5-1a mpich-1.2.5-1a-nopgi # tar xzf /root/pkgs/mpich/mpich-1.2.5-1a.tar.gz # mv mpich-1.2.5 mpich-1.2.5-1a-pgi # rm -fv mpich # ln -sv mpich-1.2.5-1a-pgi mpich # cd mpich # export F90=pgf90 F77=pgf77 CC=pgcc # ./configure --with-device=ch_p4 --with-arch=LINUX --enable-long-double --enable-f90modules --with-mpe -lib=-L/opt/pgi/linux86/lib # make That takes care of MPICH. Now, in the CPMD source folder, just do: # ./Configure PC-PGI-MPI > Makefile # make and viola!, you should have MPI parallel CPMD. I've also attached a gzip'd copy of the PC-PGI-MPI makefile I generated and used. It may contain paths that are specific to my setup so be careful using it. Hope this helps. Jim On Wednesday 20 August 2003 10:16 pm, you wrote: > Dear Jim, > > Do you have included the way of compiling CPMD in the list? I > couldn?t find the way of doing it, but I still experiencing the same > problems you had. Could you send me the Makefile you have used, as well as > giving me any clues/trics of how to make MPI and CPMD work together using > PGI? I thank you vey much in advance. > > Best wishes > > Pierre > > Prof. Pierre Moth? Esteves > Department of Organic Chemistry > Institute of Chemistry > Universidade Federal do Rio de Janeiro (UFRJ) > Cidade Universit?ria - Ilha do Fund?o > Centro de Tecnologia - Bloco A > Rio de Janeiro - RJ 21949-900 > Brazil > email: pesteves at iq.ufrj.br > Tel.: 55-21-2562-7363 > FAX: 55-21-2562-7106 > > > ----- Original Message ----- > From: "Jim Kress" > To: > Cc: > Sent: Monday, August 18, 2003 9:14 PM > Subject: [CPMD-list] OpenMP Parallelization of CPMD > > > I have managed to get CPMD 3.7.2 running in parallel using MPI (MPICH) > > and > > the > > > Portland Group Compilers (Thanks Axel!). I'd like to try to get it to > > run > > in > > > parallel with OpenMP to compare performance with MPI (MPICH). > > > > The CPMD documentation alludes to OpenMP but gives no directions on how > > to > > do > > > the necessary compiles. Also, Configure has no (obvious) information on > > how > > > to create an OpenMP parallel version of CPMD. > > > > Anybody know how to do this and is willing to share with the list? > > > > Thanks. > > > > Jim > > _______________________________________________ > > CPMD-list mailing list > > CPMD-list at cpmd.org > > http://www.cpmd.org/mailman/listinfo/cpmd-list ------------------------------------------------------- -------------- next part -------------- A non-text attachment was scrubbed... Name: Makefile.gz Type: text/x-makefile Size: 19173 bytes Desc: not available Url : http://cpmd.org/pipermail/cpmd-list/attachments/20030820/04f324c8/attachment.bin From ct at chemie.hu-berlin.de Thu Aug 21 09:24:51 2003 From: ct at chemie.hu-berlin.de (Christian Tuma) Date: Thu, 21 Aug 2003 09:24:51 +0200 Subject: [CPMD-list] How to modify results more reasonable? In-Reply-To: <000001c367b0$b4ede360$d2137fca@pc26> References: <20030818112435.B32482085FC@mail.shcnc.ac.cn> <20030820102054.GC27959@uranus.chemie.hu-berlin.de> <000001c367b0$b4ede360$d2137fca@pc26> Message-ID: <20030821072451.GA28894@uranus.chemie.hu-berlin.de> Dear Rongjian, I took one more look at your sample input file: You calculated your system under true periodic boundary conditions using "SYMMETRY 1" ! This can be a problem when you have a charged system. Here you better use "SYMMETRY 0", this way interactions between (charged) periodic images should not occur. The keyword "ISOLATED MOLECULE" affects the number of internal degrees of freedom considered in a numerical vibrational analysis if I remember correctly. So if you use "SYMMETRY 0" you will hopefully get the same answer as from GaussianXX (using BLYP as well). Good luck, Christian. -- Christian Tuma Humboldt-Universitaet Berlin ct at chemie.hu-berlin.de Arbeitsgruppe Quantenchemie (Prof. Sauer) phone: +49-30-20937140 Brook-Taylor-Str. 2, 12489 Berlin, GERMANY fax: +49-30-20937136 http://www.chemie.hu-berlin.de/ag_sauer From wyin at mail.unomaha.edu Fri Aug 22 00:17:16 2003 From: wyin at mail.unomaha.edu (Weiguo Yin) Date: Thu, 21 Aug 2003 17:17:16 -0500 Subject: [CPMD-list] static relaxation of crystal structure Message-ID: Hello, list: Please let me know whether there is a simple input to perform static relaxation of crystal structure, i.e., the lattice constants and/or unit cell shape, using CPMD. I cannot find it in the manual. Do I have to do it dynamically? I would appreciate your help. Weiguo Yin ---- Department of Physics University of Nebraska at Omaha Omaha, NE 68182 U.S.A. TEL: (402) 554 3730 FAX: (402) 554 3100 E-mail: wyin at mail.unomaha.edu From krauthau at CCM.UDel.Edu Sun Aug 24 20:32:20 2003 From: krauthau at CCM.UDel.Edu (krauthau at CCM.UDel.Edu) Date: Sun, 24 Aug 2003 13:32:20 EST Subject: [CPMD-list] A question about energy bands Message-ID: <200308241832.OAA03828@CCM.UDel.Edu> An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://cpmd.org/pipermail/cpmd-list/attachments/20030824/73d5f661/attachment.cc From krauthau at ccm.udel.edu Mon Aug 25 22:53:00 2003 From: krauthau at ccm.udel.edu (Carl Krauthauser) Date: Mon, 25 Aug 2003 16:53:00 -0400 Subject: [CPMD-list] A problem with ENERGYBANDS Message-ID: <3F4A772C.6020505@ccm.udel.edu> Dear CPMD users, I am attempting to extract the energy bands as a function of the k-vector for a particular rigid-rod polymer in a triclinic lattice. I have used the following script, which if I understand the manual correctly, should give me the desired information. However, I do not seem to get the promised ENERGYBANDS file. Does anyone know what I am doing wrong or omitting? Thank you all for your assistance! Carl > &CPMD > ! OPTIMIZE WAVEFUNCTION > ENERGYBANDS > &END > ! > ! Becke88-Perdew86 > ! > &DFT > FUNCTIONAL BP > GC CUTOFF 1.0E-5 > &END > ! > ! Cell parameters > ! > &SYSTEM > ANGSTROM > SYMMETRY > 14 > CELL > 6.54 0.532 1.836 0.0 -0.307 -0.266 > CUTOFF > 55.0 > &END > ! > ! Reaction core is formed by the first four carbons > ! > &ATOMS > *O_MT_GIA_BLYP KLEINMANN-BYLANDER RAGGIO=1.0 > 1 1 9 > 4 > 1.321 0.007 2.006 > -1.328 0.010 -1.982 > 4.591 1.747 2.006 > -4.598 1.750 -1.982 > *N_MT_GIA_BLYP KLEINMANN-BYLANDER RAGGIO=1.0 > 1 1 9 > 10 > 0.746 0.177 6.485 > 0.582 0.181 8.791 > -0.615 -0.153 8.107 > -0.602 -0.254 3.231 > 0.589 0.111 3.975 > 4.016 1.917 6.485 > 3.328 1.921 8.791 > 2.655 1.587 8.107 > 2.668 1.486 3.231 > 3.859 1.851 3.975 > *C_MT_GIA_BLYP KLEINMANN-BYLANDER RAGGIO=1.0 > 1 1 9 > 26 > 0.360 0.090 7.398 > -0.007 0.031 9.224 > -0.399 -0.122 6.978 > -0.804 -0.254 5.549 > -0.399 -0.167 4.624 > 0.360 0.052 5.092 > 0.000 -0.063 2.834 > -0.013 -0.032 1.429 > 0.634 0.021 1.057 > 0.680 0.059 -0.300 > 0.000 0.028 -1.381 > -0.647 -0.003 -1.021 > -0.693 -0.028 0.348 > 3.630 1.830 7.398 > 3.263 1.771 9.224 > 2.871 1.618 6.978 > 2.466 1.486 5.549 > 2.871 1.573 4.624 > 3.630 1.792 5.092 > 3.270 1.677 2.834 > 3.257 1.708 1.429 > 3.904 1.761 1.057 > 3.950 1.761 -0.300 > 3.270 1.768 -1.381 > 2.623 1.737 -1.021 > 2.577 1.712 0.348 > *H_GIA_BLYP KLEINMANN-BYLANDER RAGGIO=1.0 > 0 0 9 > 14 > 1.386 -0.056 3.015 > -1.393 0.010 -2.990 > 1.086 0.334 9.356 > -1.092 -0.435 2.630 > 1.158 0.104 -0.528 > -1.177 -0.049 0.576 > -1.354 -0.400 5.224 > 4.656 1.684 3.015 > 1.877 1.750 -2.990 > 4.356 2.074 9.356 > 2.178 1.305 2.630 > 4.428 1.844 -0.528 > 2.093 1.691 0.576 > 1.916 1.340 5.224 > &END -- __________________________________________________________ Carl Krauthauser, Ph.D. Research Associate University of Delaware - Center for Composite Materials 215 Composites Manufacturing Sciences Lab Newark, Delaware 19716-3144 Phone:(302) 831-8701 FAX: (302) 831-8525 e-mail: krauthau at ccm.udel.edu From piana at power.curtin.edu.au Tue Aug 26 04:37:35 2003 From: piana at power.curtin.edu.au (Stefano Piana) Date: Tue, 26 Aug 2003 10:37:35 +0800 Subject: [CPMD-list] Optimization of cell parameters. In-Reply-To: <200308202038.47321.jimkress@kressworks.com> References: <200308202038.47321.jimkress@kressworks.com> Message-ID: <3F4AC7EF.6020905@power.curtin.edu.au> Hi, I am trying to run an optimization of geometry and cell parameters (I have attached at the end of this mail the input file). The calculation runs fine for the first part, however, when it comes close to the end it never converges. It could simply be the steepest descent algorithm that is not good enough, however the variation of the total energy with respect to the cell size, in the final part of the calculation worries me a bit. In practice, if the volume versus total energy is plotted, there is a linear relationship between total energy and very small changes in the cell size: Etot = E0 + a*(V-V0) where, in this case, a = 0.05 Hartree/au^3; V0 = 2406.1 au^3; E0 = -244.044 Hartree This behaviour makes me wornder if there is any inconsistency in the calculation of the stress tensor. A shrinkage of the cell makes the plane waves basis set intrinsically better, however I am quite surprised to see an energy difference of 3 kcal/mol for a variation of 0.001% (2.0e-4 au) in the cell parameters. I attach to the mail the input file and the volume with corresponding energy calculated for the last step of the geometry optimization (file pip). Thanks for any comment/suggestion/help, Stefano This is the input file I use: ---------------------------------------------------- &CPMD OPTIMIZE GEOMETRY PARRINELLO-RAHMAN TSDC LANCZOS DIAGONALISATION LANCZOS PARAMETERS 1 6 10 1.d-8 SPLINE RANGE 6.0 SPLINE POINTS 3000 MAXSTEP 10000 RESTFILE 2 &END &SYSTEM POISSON TUCKERMAN SYMMETRY 14 CHARGE 0.0 CELL DEGREES 9.811000 0.708694 0.541739 90.000000 91.580000 90.000000 CUTOFF 70.0 ANGSTROM KPOINTS MONKHORST-PACK 1 1 1 TESR 4 4 4 &END [ Atom and System section follows ] ---------------------------- -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: pip Url: http://cpmd.org/pipermail/cpmd-list/attachments/20030826/e9b1330c/attachment.cc From pesteves at iq.ufrj.br Tue Aug 26 22:13:04 2003 From: pesteves at iq.ufrj.br (=?iso-8859-1?Q?Pierre_Moth=E9_Esteves?=) Date: Tue, 26 Aug 2003 17:13:04 -0300 Subject: [CPMD-list] OpenMP Parallelization of CPMD References: <200308202038.47321.jimkress@kressworks.com> Message-ID: <08f801c36c0e$74f01960$d31ea492@boltzmann> Dear Jim and CPMD list members, I did what you suggested, but it seems that it still not working. Now I got problems with some pointers. My cluster has dual Athlons MP 2.0+ machines. Attached you can find my Makefile. Below you will find the error I got. Any suggestions? In any case, many thanks in advance for your help, both Jim and CPMD list members. Best wishes to all, Prof. Pierre Moth? Esteves Department of Organic Chemistry Institute of Chemistry Universidade Federal do Rio de Janeiro (UFRJ) Cidade Universit?ria - Ilha do Fund?o Centro de Tecnologia - Bloco A Rio de Janeiro - RJ 21949-900 Brazil email: pesteves at iq.ufrj.br Tel.: 55-21-2562-7363 FAX: 55-21-2562-7106 ---------------------------------------------------------------------------- ------------------------------------------------ make: *** Warning: File `cpmd.F' has modification time in the future (2003-07-26 13:54:52 > 2000-07-29 07:15:37) rm -f cpmd.f /lib/cpp -P -C -traditional -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT -DPARAL LEL -DMP_LIBRARY=__MPI -DMYRINET ./cpmd.F ./cpmd.f mpif77 -c -fast -Mr8 -byteswapio -Msignextend -Msecond_underscore ./cpmd.f -o ./cpmd.o f771: Unrecognized option `-fast' In file included from ./cpmd.f:11: system.h: In subroutine `cpmd': system.h:76: POINTER (IP_NKPBL,NKPBL),(IP_KPBEG,KPBEG) 1 2 Unrecognized statement name at (1) and invalid form for assignment or statement-function definition at (2) system.h:183: POINTER (IP_MAPGP,MAPGP) 1 2 Unrecognized statement name at (1) and invalid form for assignment or statement-function definition at (2) system.h:195: POINTER(IP_IATPT,IATPT),(IP_IPEPT,IPEPT),(IP_IATPE,IATPE) 1 2 Unrecognized statement name at (1) and invalid form for assignment or statement-function definition at (2) system.h:473: POINTER (IP_NASSEL,NASSEL) 1 2 Unrecognized statement name at (1) and invalid form for assignment or statement-function definition at (2) In file included from ./cpmd.f:13: prop.inc:52: POINTER (IP_ICUBEORB,ICUBEORB),(IP_Z_11,Z_11) 1 2 Unrecognized statement name at (1) and invalid form for assignment or statement-function definition at (2) system.h:77: COMMON/NKIP/ IP_NKPBL,IP_KPBEG 1 ./cpmd.f:22: (continued): CALL SIGNAL(24,SOFTEX,-1) 2 Invalid declaration of or reference to symbol `ip_nkpbl' at (2) [initially seen at (1)] system.h:77: COMMON/NKIP/ IP_NKPBL,IP_KPBEG 1 ./cpmd.f:22: (continued): CALL SIGNAL(24,SOFTEX,-1) 2 Invalid declaration of or reference to symbol `ip_kpbeg' at (2) [initially seen at (1)] system.h:184: COMMON/MAPP/ IP_MAPGP 1 ./cpmd.f:22: (continued): CALL SIGNAL(24,SOFTEX,-1) 2 Invalid declaration of or reference to symbol `ip_mapgp' at (2) [initially seen at (1)] system.h:196: COMMON/ATPT/NATPE,NORBPE,IP_IATPT,IP_IPEPT,IP_IATPE 1 ./cpmd.f:22: (continued): CALL SIGNAL(24,SOFTEX,-1) 2 Invalid declaration of or reference to symbol `ip_iatpt' at (2) [initially seen at (1)] system.h:196: COMMON/ATPT/NATPE,NORBPE,IP_IATPT,IP_IPEPT,IP_IATPE 1 ./cpmd.f:22: (continued): CALL SIGNAL(24,SOFTEX,-1) 2 Invalid declaration of or reference to symbol `ip_ipept' at (2) [initially seen at (1)] system.h:196: COMMON/ATPT/NATPE,NORBPE,IP_IATPT,IP_IPEPT,IP_IATPE 1 ./cpmd.f:22: (continued): CALL SIGNAL(24,SOFTEX,-1) 2 Invalid declaration of or reference to symbol `ip_iatpe' at (2) [initially seen at (1)] system.h:476: COMMON/SSEL2/ IP_NASSEL 1 ./cpmd.f:22: (continued): CALL SIGNAL(24,SOFTEX,-1) 2 Invalid declaration of or reference to symbol `ip_nassel' at (2) [initially seen at (1)] prop.inc:54: & NUM_CUBEORB,IP_ICUBEORB 1 ./cpmd.f:22: (continued): CALL SIGNAL(24,SOFTEX,-1) 2 Invalid declaration of or reference to symbol `ip_icubeorb' at (2) [initially seen at (1)] ./cpmd.f:22: CALL SIGNAL(24,SOFTEX,-1) ^ Too many arguments passed to intrinsic `SIGNAL' at (^) ./cpmd.f:23: CALL SIGNAL(30,SOFTEX,-1) ^ Too many arguments passed to intrinsic `SIGNAL' at (^) ./cpmd.f:24: CALL SIGNAL(1,SOFTEX,-1) ! SIGHUP(1), SIGUSR1 (10) and SIGUSR ^ Too many arguments passed to intrinsic `SIGNAL' at (^) ./cpmd.f:25: CALL SIGNAL(10,SOFTEX,-1) ! be caught. VERY useful for queuing ^ Too many arguments passed to intrinsic `SIGNAL' at (^) ./cpmd.f:26: CALL SIGNAL(12,SOFTEX,-1) ^ Too many arguments passed to intrinsic `SIGNAL' at (^) system.h:75: INTEGER NKPBL(*),KPBEG(*) 1 ./cpmd.f:195: (continued): END 2 Invalid declaration of or reference to symbol `nkpbl' at (2) [initially seen at (1)] system.h:75: INTEGER NKPBL(*),KPBEG(*) 1 ./cpmd.f:195: (continued): END 2 Invalid declaration of or reference to symbol `kpbeg' at (2) [initially seen at (1)] system.h:182: INTEGER MAPGP(*) 1 ./cpmd.f:195: (continued): END 2 Invalid declaration of or reference to symbol `mapgp' at (2) [initially seen at (1)] system.h:193: INTEGER NATPE,NORBPE,IATPT,IPEPT,IATPE 1 ./cpmd.f:195: (continued): END 2 Invalid declaration of or reference to symbol `iatpt' at (2) [initially seen at (1)] system.h:193: INTEGER NATPE,NORBPE,IATPT,IPEPT,IATPE 1 ./cpmd.f:195: (continued): END 2 Invalid declaration of or reference to symbol `iatpe' at (2) [initially seen at (1)] system.h:474: INTEGER NASSEL(*) 1 ./cpmd.f:195: (continued): END 2 Invalid declaration of or reference to symbol `nassel' at (2) [initially seen at (1)] prop.inc:50: INTEGER ICUBEORB(*) 1 ./cpmd.f:195: (continued): END 2 Invalid declaration of or reference to symbol `icubeorb' at (2) [initially seen at (1)] f77: file path prefix `/usr/lib/gcc-lib/yteswapio/2.96/' never used make: *** [cpmd.o] Error 1 ----- Original Message ----- From: "Jim Kress" To: Cc: Sent: Wednesday, August 20, 2003 5:38 PM Subject: Fwd: Re: [CPMD-list] OpenMP Parallelization of CPMD Here is a copy of the email I sent to Pierre in response to his question about CPMD MPI with PGI. It may be of some use to others who are trying to do this compile. Jim ---------- Forwarded Message ---------- Subject: Re: [CPMD-list] OpenMP Parallelization of CPMD Date: Wed, 20 Aug 2003 20:35:45 +0000 From: Jim Kress To: Pierre Moth? Esteves Dear Pierre, The secret to compiling CPMD with MPI (MPICH) using the Portland Group compilers is to make sure you have compiled your MPI code with the same set of compilers. In my case, the MPI code was MPICH. To configure MPICH with pgi: # su -l root # cd /opt # mv mpich-1.2.5-1a mpich-1.2.5-1a-nopgi # tar xzf /root/pkgs/mpich/mpich-1.2.5-1a.tar.gz # mv mpich-1.2.5 mpich-1.2.5-1a-pgi # rm -fv mpich # ln -sv mpich-1.2.5-1a-pgi mpich # cd mpich # export F90=pgf90 F77=pgf77 CC=pgcc # ./configure --with-device=ch_p4 --with-arch=LINUX --enable-long-double --enable-f90modules --with-mpe -lib=-L/opt/pgi/linux86/lib # make That takes care of MPICH. Now, in the CPMD source folder, just do: # ./Configure PC-PGI-MPI > Makefile # make and viola!, you should have MPI parallel CPMD. I've also attached a gzip'd copy of the PC-PGI-MPI makefile I generated and used. It may contain paths that are specific to my setup so be careful using it. Hope this helps. Jim On Wednesday 20 August 2003 10:16 pm, you wrote: > Dear Jim, > > Do you have included the way of compiling CPMD in the list? I > couldn?t find the way of doing it, but I still experiencing the same > problems you had. Could you send me the Makefile you have used, as well as > giving me any clues/trics of how to make MPI and CPMD work together using > PGI? I thank you vey much in advance. > > Best wishes > > Pierre > > Prof. Pierre Moth? Esteves > Department of Organic Chemistry > Institute of Chemistry > Universidade Federal do Rio de Janeiro (UFRJ) > Cidade Universit?ria - Ilha do Fund?o > Centro de Tecnologia - Bloco A > Rio de Janeiro - RJ 21949-900 > Brazil > email: pesteves at iq.ufrj.br > Tel.: 55-21-2562-7363 > FAX: 55-21-2562-7106 > > > ----- Original Message ----- > From: "Jim Kress" > To: > Cc: > Sent: Monday, August 18, 2003 9:14 PM > Subject: [CPMD-list] OpenMP Parallelization of CPMD > > > I have managed to get CPMD 3.7.2 running in parallel using MPI (MPICH) > > and > > the > > > Portland Group Compilers (Thanks Axel!). I'd like to try to get it to > > run > > in > > > parallel with OpenMP to compare performance with MPI (MPICH). > > > > The CPMD documentation alludes to OpenMP but gives no directions on how > > to > > do > > > the necessary compiles. Also, Configure has no (obvious) information on > > how > > > to create an OpenMP parallel version of CPMD. > > > > Anybody know how to do this and is willing to share with the list? > > > > Thanks. > > > > Jim > > _______________________________________________ > > CPMD-list mailing list > > CPMD-list at cpmd.org > > http://www.cpmd.org/mailman/listinfo/cpmd-list ------------------------------------------------------- --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.512 / Virus Database: 309 - Release Date: 8/23/2003 -------------- next part -------------- An embedded message was scrubbed... From: root Subject: no subject Date: Sat, 29 Jul 2000 07:24:01 -0300 Size: 127897 Url: http://cpmd.org/pipermail/cpmd-list/attachments/20030826/e1fd7c60/attachment.eml From veronique.vanspeybroeck at ugent.be Wed Aug 27 11:42:29 2003 From: veronique.vanspeybroeck at ugent.be (Veronique Van Speybroeck) Date: Wed, 27 Aug 2003 11:42:29 +0200 Subject: [CPMD-list] [Fwd: [Fwd: Re: Benchmark IBM pSeries]] Message-ID: <3F4C7D05.3060809@ugent.be> Dear all, We are planning to buy a new machine to run large CPMD calculations. Therefore some benchmarks are done for us at the benchmark center of IBM in Montpellier. They have run some examples of our input files and encounterd strange error messages. The output file is attached. Has somebody encountered analogous things? Maybe it has something to do with the 64 bit version of the code. Has somebody have good experiences or suggestions running CPMD jobs on 64 bit machines. The available budget is around 100000 Euros. Thanks Veronique -------- Original Message -------- Subject: [Fwd: Re: Benchmark IBM pSeries] Date: Wed, 27 Aug 2003 10:06:37 +0200 From: "Colin Dumontier" To: veronique.vanspeybroeck at ugent.be CC: "Eric Michel" , "Sophie Vilarem" , Gerd_Vanmechelen/Belgium/IBM%IBMFR Dear Veronique, We are having difficulties running the RUG input decks for CPMD. We used the provided uspp generation program to create the following atoms files, and moved them to the run directory, where the CPMD input decks reside : -rw-r--r-- 1 rug staff 35916 Aug 26 17:24 001-H-ca--bm.uspp -rw-r--r-- 1 rug staff 98088 Aug 26 17:26 006-C-ca--bm.uspp -rw-r--r-- 1 rug staff 99432 Aug 26 17:27 007-N-ca--bm.uspp -rw-r--r-- 1 rug staff 100776 Aug 26 17:26 008-O-ca--bm.uspp -rw-r--r-- 1 rug staff 109704 Aug 26 17:27 015-P-ca--vgrp.uspp -rw-r--r-- 1 rug staff 210612 Aug 26 17:28 019-K-ca-sp-vgrp.uspp -rw-r--r-- 1 rug staff 232196 Aug 26 17:28 045-Rh-gpw-n-campos.uspp After succesfully configuring and compiling the MPI code for an IBM 64bit platform, we submitted the Rh.wf.inp input deck (wavefunction optimization). The job crashed after several hours, and didn't generate a RESTART file that I assume would have been used for the Rh.damp.inp submission. Here is the log file : (See attached file: Rh.wf.out) Are we doing something wrong here ? Thanks a lot. Best regards. __________________________________________ Colin DUMONTIER (cdumontier at fr.ibm.com) IBM Scientific & Technical Computing EMEA ATS - P.S.S.C / Dpt 1459 / Montpellier FRANCE Tel: +33 4 67 34 42 37 Fax: +33 4 67 34 64 77 http://w3.pssc.mop.ibm.com ----- Forwarded by Colin Dumontier/France/IBM on 27-08-03 10:03 ----- Eric Michel To: Colin Dumontier/France/IBM at IBMFR 27-08-03 10:04 cc: From: Eric Michel/France/IBM at IBMFR Subject: [Fwd: Re: Benchmark IBM pSeries] Eric Michel IBM Scientific & Technical Computing EMEA ATS-P.S.S.C/ Monptellier FRANCE emichel at fr.ibm.com - +33-467344731 ----- Forwarded by Eric Michel/France/IBM on 27-08-03 10:04 ----- Veronique Van Speybroeck To: Gerd Vanmechelen/Belgium/IBM at IBMBE, Eric Michel/France/IBM at IBMFR Subject: [Fwd: Re: Benchmark IBM pSeries] 25-08-03 12:07 Dear Gerd, Eric Michel, concerning the benchmarks following arrangements were made. We have set up an http server : moldyn10.ugent.be http://moldyn10.ugent.be there you can find three links refering to the CPMD code the code for the pseudopotentials and the input files. To compile the CPMD code, you must go to the directory SOURCE en let run the file Configure with the correct option . More details are given in the file itself. Bv. Configure IBM-SP4-64 > Makefile. then the code can be compiled using the standard make commandos. To run the CPMD code one also needs pseudopotential files, which have a binary format and thus have to be generated on the machine the benchmarks are run. To compile this code you go to the directory source and again run the makefile. I will give more details about how the input files have to be run once you give me a sign that you compiled the codes succesfully. Best regards, thanks in advance veronique -------- Original Message -------- Subject: Re: Benchmark IBM pSeries Date: Mon, 25 Aug 2003 10:22:03 +0200 From: Veronique Van Speybroeck To: Gerd Vanmechelen , emichel at fr.ibm.com References: Beste Gerd, we zullen de code beschikbaar stellen via een http server nl. de moldyn10.ugent.be: http://moldyn10.ugent.be Dit zal vanmiddag beschikbaar zijn. Gezien de codes normaal niet mogen gedistribueerd worden zullen wij vanavond de site weer dicht zetten. Hopelijk kunnen jullie de code afhalen deze middag. Het betreft twee tar files : cpmdv37_1.tar : Dit is de CPMD code waarvan de benchmarks moeten gelopen worden. Om te compileren ga naar de directory SOURCE. Daar staat een file Configure . Daar kan je een makefile aan maken voor het programma te compileren. Bv. Configure IBM-SP4-64 > Makefile. Een je dat hebt kan je de code compileren. en uspp-734-3.tgz : Dit is een programma op pseudopotentiaalfiles aan te maken die nodig zijn om het voorgaande programma te laten lopen. Eens het untard is ga je naar de directory Source en compileer je het programma. De inputfiles die we wensen te laten lopen zullen ook op de site staan. Eens jullie de code goed afgehaald hebben, kan je mij een seintje geven en dan geef ik verdere instructies over wat precies moet gebeuren om de code te doen draaien. Alvast bedankt veronique PS : Als je liever hebt dat ik deze mail in het engels opmaak voor Eric Michel geef dan een seintje Gerd Vanmechelen wrote: >V?ronique, > >Zoals besproken zullen onze Scientific & Technical computing >specialisten in Montpellier jullie fortran programmas testen. > >Kan je een FTP account aanmaken ? > >De persoon die de code zal downloaden is Eric Michel (EMICHEL at fr.ibm.com) > >Ter info : http://www-1.ibm.com/servers/eserver/briefingcenter/mbc/ > >Als je nog opmerkingen hebt bij de manier waarop de testen moeten verlopen >kan je deze per mail bezorgen, met Eric in copie. > > >Regards > >Gerd Vanmechelen, Sales Specialist >IBM Belgium / Luxembourg Systems Sales >Tel : 0032-2-2253569 Fax : 0032-2-2252368 >E-mail : Gerd_Vanmechelen at be.ibm.com > > > > -- ?????? -- ?????? -- ?????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20030827/0ff6d391/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: Rh.wf.out Type: application/octet-stream Size: 55442 bytes Desc: not available Url : http://cpmd.org/pipermail/cpmd-list/attachments/20030827/0ff6d391/attachment.obj From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Wed Aug 27 12:08:48 2003 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Wed, 27 Aug 2003 12:08:48 +0200 Subject: [CPMD-list] (no subject) Message-ID: <200308271008.h7RA8mQ19515@yello.theochem.ruhr-uni-bochum.de> PE> Dear Jim and CPMD list members, hi pierre, PE> I did what you suggested, but it seems that it still not PE> working. Now I got problems with some pointers. My cluster has dual Athlons PE> MP 2.0+ machines. Attached you can find my Makefile. Below you will find the PE> error I got. Any suggestions? In any case, many thanks in advance for your PE> help, both Jim and CPMD list members. if you are not locked into using MPICH, you can try one of the ready-to-use, CPMD compatible(TM) lam-mpi rpms i have put up for download at: they include proper mpi wrappers for intel ifc, portland pgf77 and pgf90. to avoid collisions or confusion, you should remove all traces of the existing MPICH installation first, though. but let's take a closer look at you error messages. PE> Best wishes to all, PE> Prof. Pierre Moth? Esteves PE> Department of Organic Chemistry PE> Institute of Chemistry PE> Universidade Federal do Rio de Janeiro (UFRJ) PE> Cidade Universit?ria - Ilha do Fund?o PE> Centro de Tecnologia - Bloco A PE> Rio de Janeiro - RJ 21949-900 PE> Brazil PE> email: pesteves at iq.ufrj.br PE> Tel.: 55-21-2562-7363 PE> FAX: 55-21-2562-7106 PE> ---------------------------------------------------------------------------- PE> ------------------------------------------------ PE> make: *** Warning: File `cpmd.F' has modification time in the future you have unsynchronized system times between your compilation machine and the NFS server. you should consider using a programm package like NTP (cf. http://www.ntp.org/). there are ready to use packages included in most linux distributions. this has _nothing_ to do with you problem, though. PE> (2003-07-26 13:54:52 > 2000-07-29 07:15:37) PE> rm -f cpmd.f PE> /lib/cpp -P -C -traditional -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT -DPARAL PE> LEL -DMP_LIBRARY=__MPI -DMYRINET ./cpmd.F ./cpmd.f PE> mpif77 -c -fast -Mr8 -byteswapio -Msignextend -Msecond_underscore PE> ./cpmd.f -o ./cpmd.o PE> f771: Unrecognized option `-fast' PE> In file included from ./cpmd.f:11: PE> system.h: In subroutine `cpmd': PE> system.h:76: PE> POINTER (IP_NKPBL,NKPBL),(IP_KPBEG,KPBEG) PE> 1 2 PE> Unrecognized statement name at (1) and invalid form for assignment or PE> statement-function definition at (2) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ yep this is a clear indication, that you are still using an MPICH installation that is configured to use the GNU g77 instead of pgf77. [...] PE> DEST = . PE> BIN = . PE> #QMMM_FLAGS = -D__QMECHCOUPL PE> #QMMM_LIBS = -L. -lmm PE> FFLAGS = -Mr8 -byteswapio -Msignextend -Msecond_underscore ^^^^^^^^^^^^ you don't need this, if you have compiled your MPICH package properly for pgf77/pgf90 (in fact you will get unresolved symbols on linking). you only need this flag if your MPICH package was compiled for g77. PE> LFLAGS = -llapack -lblas -byteswapio $(QMMM_LIBS) ^^^^^^^ you only need this, if you wante to read restarts that were written on a big-endian machine (like an IBM or SUN workstation). instead of the PGI supplied lapack and blas libraries (which give a horrible performance) you should try the atlas library. ready-to-use binaries for several x86 platforms are at PE> CFLAGS = PE> CPP = /lib/cpp -P -C -traditional PE> CPPFLAGS = -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT \ PE> -DPARALLEL -DMP_LIBRARY=__MPI -DMYRINET PE> NOOPT_FLAG = PE> CC = mpicc -O2 -Wall PE> FC = mpif77 -c -fast PE> LD = mpif77 -fast as a last resort, you may want to try : FC=pgf77 -I/path/to/your/local/mpich/installation/include -Msecond_underscore LD=pgf77 LFLAGS = -L/path/to/your/local/mpich/installation/lib -lfmpich -lmpich -L. -latlas $(QMMM_LIBS) which will try to use a g77 configured mpich installation. i have not tested this, but made an educated guess from looking at an old MPICH installation. hope this helps, axel kohlmeyer. PE> ------=_NextPart_000_08F5_01C36BF5.4F8D5D90-- PE> _______________________________________________ PE> CPMD-list mailing list PE> CPMD-list at cpmd.org PE> http://www.cpmd.org/mailman/listinfo/cpmd-list -- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From Ari.P.Seitsonen at iki.fi Wed Aug 27 18:22:33 2003 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Wed, 27 Aug 2003 18:22:33 +0200 Subject: [CPMD-list] A problem with ENERGYBANDS In-Reply-To: <3F4A772C.6020505@ccm.udel.edu> (message from Carl Krauthauser on Mon, 25 Aug 2003 16:53:00 -0400) References: <3F4A772C.6020505@ccm.udel.edu> Message-ID: <200308271622.h7RGMX416248@magadino.cscs.ch> Dear Carl, It looks to me as if that option "ENERGYBANDS" would only work if KPOINTS are explicitly defined in the input; please see the beginning of the source file 'rinit.F', the value of the variable 'TKPNT' has to be '.TRUE.'. Greetings from Bayreuth, today again from Zurich, apsi > Dear CPMD users, > > I am attempting to extract the energy bands as a function of the > k-vector for a particular rigid-rod polymer in a triclinic lattice. I > have used the following script, which if I understand the manual > correctly, should give me the desired information. However, I do not > seem to get the promised ENERGYBANDS file. Does anyone know what I am > doing wrong or omitting? Thank you all for your assistance! > > > Carl > > > &CPMD > > ! OPTIMIZE WAVEFUNCTION > > ENERGYBANDS > > &END > > ! > > ! Becke88-Perdew86 > > ! > > &DFT > > FUNCTIONAL BP > > GC CUTOFF 1.0E-5 > > &END > > ! > > ! Cell parameters > > ! > > &SYSTEM > > ANGSTROM > > SYMMETRY > > 14 > > CELL > > 6.54 0.532 1.836 0.0 -0.307 -0.266 > > CUTOFF > > 55.0 > > &END > > ! > > ! Reaction core is formed by the first four carbons > > ! > > &ATOMS > > *O_MT_GIA_BLYP KLEINMANN-BYLANDER RAGGIO=1.0 > > 1 1 9 > > 4 > > 1.321 0.007 2.006 > > -1.328 0.010 -1.982 > > 4.591 1.747 2.006 > > -4.598 1.750 -1.982 > > *N_MT_GIA_BLYP KLEINMANN-BYLANDER RAGGIO=1.0 > > 1 1 9 > > 10 > > 0.746 0.177 6.485 > > 0.582 0.181 8.791 > > -0.615 -0.153 8.107 > > -0.602 -0.254 3.231 > > 0.589 0.111 3.975 > > 4.016 1.917 6.485 > > 3.328 1.921 8.791 > > 2.655 1.587 8.107 > > 2.668 1.486 3.231 > > 3.859 1.851 3.975 > > *C_MT_GIA_BLYP KLEINMANN-BYLANDER RAGGIO=1.0 > > 1 1 9 > > 26 > > 0.360 0.090 7.398 > > -0.007 0.031 9.224 > > -0.399 -0.122 6.978 > > -0.804 -0.254 5.549 > > -0.399 -0.167 4.624 > > 0.360 0.052 5.092 > > 0.000 -0.063 2.834 > > -0.013 -0.032 1.429 > > 0.634 0.021 1.057 > > 0.680 0.059 -0.300 > > 0.000 0.028 -1.381 > > -0.647 -0.003 -1.021 > > -0.693 -0.028 0.348 > > 3.630 1.830 7.398 > > 3.263 1.771 9.224 > > 2.871 1.618 6.978 > > 2.466 1.486 5.549 > > 2.871 1.573 4.624 > > 3.630 1.792 5.092 > > 3.270 1.677 2.834 > > 3.257 1.708 1.429 > > 3.904 1.761 1.057 > > 3.950 1.761 -0.300 > > 3.270 1.768 -1.381 > > 2.623 1.737 -1.021 > > 2.577 1.712 0.348 > > *H_GIA_BLYP KLEINMANN-BYLANDER RAGGIO=1.0 > > 0 0 9 > > 14 > > 1.386 -0.056 3.015 > > -1.393 0.010 -2.990 > > 1.086 0.334 9.356 > > -1.092 -0.435 2.630 > > 1.158 0.104 -0.528 > > -1.177 -0.049 0.576 > > -1.354 -0.400 5.224 > > 4.656 1.684 3.015 > > 1.877 1.750 -2.990 > > 4.356 2.074 9.356 > > 2.178 1.305 2.630 > > 4.428 1.844 -0.528 > > 2.093 1.691 0.576 > > 1.916 1.340 5.224 > > &END > > > -- > __________________________________________________________ > Carl Krauthauser, Ph.D. > Research Associate > University of Delaware - Center for Composite Materials > 215 Composites Manufacturing Sciences Lab > Newark, Delaware 19716-3144 > Phone:(302) 831-8701 > FAX: (302) 831-8525 > e-mail: krauthau at ccm.udel.edu > > > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland From symsun at hotmail.com Thu Aug 28 04:48:44 2003 From: symsun at hotmail.com (Sun Yuming) Date: Thu, 28 Aug 2003 10:48:44 +0800 Subject: [CPMD-list] Problems with linking CPMD3.7.2 using IFC7.1 Message-ID: Dear all, I am trying to install the cpmd3.7.2 using ifc7.1 on a Dell PE2650 server running RH9.0. To solve the "undefined reference to ctype_b" error, the libc-2.2.93 was used. Below are errors reported during linking: /lib/libpthread.so.0(*IND*+0x0): multiple definition of `pthread_cond_signal' /lib/libpthread.so.0(*IND*+0x0): multiple definition of `pthread_cond_broadcast' /lib/libpthread.so.0(.text+0xdd0): In function `pthread_cond_wait at GLIBC_2.0': : multiple definition of `pthread_cond_wait at GLIBC_2.0' /lib/libpthread.so.0(.text+0xd90): In function `pthread_cond_init at GLIBC_2.0': : multiple definition of `pthread_cond_init at GLIBC_2.0' /lib/libpthread.so.0(*IND*+0x0): multiple definition of `pthread_cond_destroy' /lib/libpthread.so.0: undefined reference to `__libc_pthread_init at GLIBC_PRIVATE' /lib/libpthread.so.0: undefined reference to `__libc_allocate_rtsig_private at GLIBC_PRIVATE' /lib/libpthread.so.0: undefined reference to `__libc_thread_freeres at GLIBC_PRIVATE' /lib/libpthread.so.0: undefined reference to `__register_atfork at GLIBC_2.3.2' /lib/libpthread.so.0: undefined reference to `__libc_current_sigrtmin_private at GLIBC_PRIVATE' /lib/libpthread.so.0: undefined reference to `__libc_current_sigrtmax_private at GLIBC_PRIVATE' Part of my makefile is SHELL = /bin/sh # #--------------- Default Configuration for PC-IFC-MPI --------------- SRC = . DEST = . BIN = . #QMMM_FLAGS = -D__QMECHCOUPL #QMMM_LIBS = -L. -lmm FFLAGS = -c -w90 -w95 -O3 -axM -ip -tpp7 LFLAGS = -L/opt/intel/mkl60/lib/32 -lmkl_lapack -lmkl_ia32 -lguide -lpthread \ -L/usr/local/mpi-ifc/ch_p4/lib -lmpich -Vaxlib $(QMMM_LIBS) CFLAGS = -c -O2 -Wall CPP = /lib/cpp -P -C -traditional CPPFLAGS = -D_MKL60 -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT \ -DPARALLEL -DMP_LIBRARY=__MPI -DMYRINET -DLINUX_IFC NOOPT_FLAG = CC = icc FC = ifc LD = ifc AR = Any suggestion would be appreciated. Thanks in advance Sun Yuming _________________________________________________________________ ???????????????????????????? MSN Messenger: http://messenger.msn.com/cn From carinabacktorp at hotmail.com Thu Aug 28 18:04:16 2003 From: carinabacktorp at hotmail.com (Carina Backtorp) Date: Thu, 28 Aug 2003 18:04:16 +0200 Subject: [CPMD-list] seednumber Message-ID: Dear all, In order to have different initial velocities, we tested to change the "seed number" which is the value of "M" in the subroutine XRANF. For example: we use 2671957 instead of 100001(default value) for the seed number. We did the same in the versions 3.5.1 and 3.5.3. But we got two different results for a MD simulation. Does anyone know why we got two different results? Can one trust the result from the version 3.5.3? Or maybe the seed number cannot be changed? One have to use the default value? This is an urgent problem for me, so if anyone can help me, I would be very grateful! best regards Carina B?cktorp _________________________________________________________________ The new MSN 8: advanced junk mail protection and 2 months FREE* http://join.msn.com/?page=features/junkmail From cur at zurich.ibm.com Thu Aug 28 18:17:45 2003 From: cur at zurich.ibm.com (Alessandro Curioni) Date: Thu, 28 Aug 2003 18:17:45 +0200 Subject: [CPMD-list] CPMD on 64 bit Message-ID: Veronique, we are running CPMD with the 64 bits allocation on Power4 since 2 years without problems. Which version did you sent for the benchmark ? Old versions had problems with uspp. If you agree, I will contact the people at Montpellier to find out the problem. Best Regards, Alessandro CURIONI, PhD Research Staff Member Computational Biochemistry and Material Science group IBM Research Division - Zurich Research Laboratory Saumerstrasse 4 8003 Rueschlikon - Switzerland e-mail: cur at zurich.ibm.com www: www.zurich.ibm.com Tel: +41-1-7248633 Fax: +41-1-7248958 From resumes at workwondersstaffing.net Thu Aug 28 23:26:21 2003 From: resumes at workwondersstaffing.net (Work Wonders Staffing) Date: Thu, 28 Aug 2003 14:26:21 -0700 Subject: [CPMD