[CPMD-list] CPMD on 64-bit Linux (openSUSE 10.3) Intel Xeon

Mon Apr 28 15:31:38 CET 2008

On Mon, 28 Apr 2008, Vladimir Stegailov wrote:

vladimir,

VS> Could you give me some hints what is the reason for the following
VS> compilation error.

hard to tell, there is still a lot of necessary information missing.

[...]

VS> After having played with different flags I feel that the error is a result
VS> of some general deficiency.

so what did you change? the best is possibly to rebuild a consistent
make file by typing:

make reconfig

then:

make clean

and then:

make

and then see what happens. right now it looks like 
something is overriding the objects variable or you
have modified the makefile outside of the configuration area.

cheers,
   axel.

VS> The making failure looks like this
VS> 
VS> $ make
VS> rm -f cpmd.f
VS> /lib/cpp -P -C -traditional -D__Linux -D__PGI -DFFT_DEFAULT -DPARALLEL
VS> -DMYRINET -DLINUX_IFC -DINTEL_MKL -DPOINTER8   ./cpmd.F ./cpmd.f
VS> mpif77  -O2 -unroll -pc64 -march=pentium3 -mtune=core2  ./cpmd.f -o
VS> /cpmd.o
VS> /tmp/ifortcXABMB.o: In function `MAIN__':
VS> /cpmd.f:(.text+0x3c): undefined reference to `softex_'
VS> /cpmd.f:(.text+0x52): undefined reference to `softex_'
VS> /cpmd.f:(.text+0x68): undefined reference to `softex_'
VS> /cpmd.f:(.text+0x7e): undefined reference to `softex_'
VS> /cpmd.f:(.text+0x94): undefined reference to `softex_'
VS> /cpmd.f:(.text+0xa7): undefined reference to `startpa_'
VS> /cpmd.f:(.text+0xb6): undefined reference to `tistart_'
VS> /cpmd.f:(.text+0xdf): undefined reference to `datum_'
VS> /cpmd.f:(.text+0x156): undefined reference to `init_fileopen_'
VS> /cpmd.f:(.text+0x15d): undefined reference to `envir_'
VS> /cpmd.f:(.text+0x164): undefined reference to `setcnst_'
VS> /cpmd.f:(.text+0x16b): undefined reference to `control_'
VS> /cpmd.f:(.text+0x172): undefined reference to `dftin_'
VS> /cpmd.f:(.text+0x179): undefined reference to `sysin_'
VS> /cpmd.f:(.text+0x180): undefined reference to `setsc_'
VS> /cpmd.f:(.text+0x187): undefined reference to `detsp_'
VS> /cpmd.f:(.text+0x18e): undefined reference to `mm_init_'
VS> /cpmd.f:(.text+0x1a3): undefined reference to `timec_'
VS> /cpmd.f:(.text+0x29c): undefined reference to `pi_mdpt_'
VS> /cpmd.f:(.text+0x2d2): undefined reference to `pm_gmopts_'
VS> /cpmd.f:(.text+0x2f2): undefined reference to `prpt_'
VS> /cpmd.f:(.text+0x2fe): undefined reference to `mdpt_'
VS> /cpmd.f:(.text+0x379): undefined reference to `response_p_'
VS> /cpmd.f:(.text+0x38a): undefined reference to `my_end_'
VS> /cpmd.f:(.text+0x3b6): undefined reference to `pi_wf_'
VS> /cpmd.f:(.text+0x3bf): undefined reference to `pm_wf_'
VS> /cpmd.f:(.text+0x3c8): undefined reference to `end_swap_'
VS> /cpmd.f:(.text+0x3cf): undefined reference to `pmaxmem_'
VS> /cpmd.f:(.text+0x3d6): undefined reference to `tipri_'
VS> /cpmd.f:(.text+0x3dd): undefined reference to `timec_'
VS> /cpmd.f:(.text+0x426): undefined reference to `ttimp_'
VS> /cpmd.f:(.text+0x437): undefined reference to `datum_'
VS> /cpmd.f:(.text+0x448): undefined reference to `prmem_'
VS> /cpmd.f:(.text+0x4c3): undefined reference to `tilimex_'
VS> /cpmd.f:(.text+0x4cf): undefined reference to `specpt_'
VS> /cpmd.f:(.text+0x4db): undefined reference to `orbhard_'
VS> /cpmd.f:(.text+0x4e7): undefined reference to `proppt_'
VS> /cpmd.f:(.text+0x4f3): undefined reference to `secdpt_'
VS> /cpmd.f:(.text+0x4ff): undefined reference to `interpt_'
VS> /cpmd.f:(.text+0x50b): undefined reference to `wfopts_'
VS> /cpmd.f:(.text+0x517): undefined reference to `gmopts_'
VS> /cpmd.f:(.text+0x523): undefined reference to `ratom_'
VS> /cpmd.f:(.text+0x52a): undefined reference to `vdwin_'
VS> /cpmd.f:(.text+0x539): undefined reference to `propin_'
VS> /cpmd.f:(.text+0x540): undefined reference to `respin_p_'
VS> /cpmd.f:(.text+0x547): undefined reference to `setsys_'
VS> /cpmd.f:(.text+0x54e): undefined reference to `genxc_'
VS> /cpmd.f:(.text+0x555): undefined reference to `numpw_'
VS> /cpmd.f:(.text+0x584): undefined reference to `nmr_para_p_'
VS> /cpmd.f:(.text+0x58b): undefined reference to `rinit_'
VS> /cpmd.f:(.text+0x592): undefined reference to `rinforce_'
VS> /cpmd.f:(.text+0x599): undefined reference to `fftprp_'
VS> /cpmd.f:(.text+0x5a0): undefined reference to `initclust_'
VS> /cpmd.f:(.text+0x5a7): undefined reference to `dg_init_'
VS> /cpmd.f:(.text+0x5ae): undefined reference to `nosalloc_'
VS> /cpmd.f:(.text+0x5b5): undefined reference to `exterp_'
VS> /cpmd.f:(.text+0x5bc): undefined reference to `setbasis_'
VS> /cpmd.f:(.text+0x5c3): undefined reference to `dqgalloc_'
VS> /cpmd.f:(.text+0x5ca): undefined reference to `setefield_'
VS> /cpmd.f:(.text+0x5d6): undefined reference to `pm_cntl_'
VS> /cpmd.f:(.text+0x5dd): undefined reference to `pm_init_'
VS> /cpmd.f:(.text+0x5e6): undefined reference to `pi_cntl_'
VS> /cpmd.f:(.text+0x5ed): undefined reference to `pi_init_'
VS> /tmp/ifortcXABMB.o: In function `cpmd_':
VS> /cpmd.f:(.text+0x601): undefined reference to `softex_'
VS> /cpmd.f:(.text+0x617): undefined reference to `softex_'
VS> /cpmd.f:(.text+0x62d): undefined reference to `softex_'
VS> /cpmd.f:(.text+0x643): undefined reference to `softex_'
VS> /cpmd.f:(.text+0x659): undefined reference to `softex_'
VS> /cpmd.f:(.text+0x66c): undefined reference to `startpa_'
VS> /cpmd.f:(.text+0x67b): undefined reference to `tistart_'
VS> /cpmd.f:(.text+0x6a4): undefined reference to `datum_'
VS> /cpmd.f:(.text+0x71b): undefined reference to `init_fileopen_'
VS> /cpmd.f:(.text+0x722): undefined reference to `envir_'
VS> /cpmd.f:(.text+0x729): undefined reference to `setcnst_'
VS> /cpmd.f:(.text+0x730): undefined reference to `control_'
VS> /cpmd.f:(.text+0x737): undefined reference to `dftin_'
VS> /cpmd.f:(.text+0x73e): undefined reference to `sysin_'
VS> /cpmd.f:(.text+0x745): undefined reference to `setsc_'
VS> /cpmd.f:(.text+0x74c): undefined reference to `detsp_'
VS> /cpmd.f:(.text+0x753): undefined reference to `mm_init_'
VS> /cpmd.f:(.text+0x768): undefined reference to `timec_'
VS> /cpmd.f:(.text+0x861): undefined reference to `pi_mdpt_'
VS> /cpmd.f:(.text+0x897): undefined reference to `pm_gmopts_'
VS> /cpmd.f:(.text+0x8b7): undefined reference to `prpt_'
VS> /cpmd.f:(.text+0x8c3): undefined reference to `mdpt_'
VS> /cpmd.f:(.text+0x93e): undefined reference to `response_p_'
VS> /cpmd.f:(.text+0x94f): undefined reference to `my_end_'
VS> /cpmd.f:(.text+0x95e): undefined reference to `pi_wf_'
VS> /cpmd.f:(.text+0x967): undefined reference to `pm_wf_'
VS> /cpmd.f:(.text+0x970): undefined reference to `end_swap_'
VS> /cpmd.f:(.text+0x977): undefined reference to `pmaxmem_'
VS> /cpmd.f:(.text+0x97e): undefined reference to `tipri_'
VS> /cpmd.f:(.text+0x985): undefined reference to `timec_'
VS> /cpmd.f:(.text+0x9ce): undefined reference to `ttimp_'
VS> /cpmd.f:(.text+0x9df): undefined reference to `datum_'
VS> /cpmd.f:(.text+0x9f0): undefined reference to `prmem_'
VS> /cpmd.f:(.text+0xa6b): undefined reference to `tilimex_'
VS> /cpmd.f:(.text+0xa77): undefined reference to `specpt_'
VS> /cpmd.f:(.text+0xa83): undefined reference to `orbhard_'
VS> /cpmd.f:(.text+0xa8f): undefined reference to `proppt_'
VS> /cpmd.f:(.text+0xa9b): undefined reference to `secdpt_'
VS> /cpmd.f:(.text+0xaa7): undefined reference to `interpt_'
VS> /cpmd.f:(.text+0xab3): undefined reference to `wfopts_'
VS> /cpmd.f:(.text+0xabf): undefined reference to `gmopts_'
VS> /cpmd.f:(.text+0xacb): undefined reference to `ratom_'
VS> /cpmd.f:(.text+0xad2): undefined reference to `vdwin_'
VS> /cpmd.f:(.text+0xae1): undefined reference to `propin_'
VS> /cpmd.f:(.text+0xae8): undefined reference to `respin_p_'
VS> /cpmd.f:(.text+0xaef): undefined reference to `setsys_'
VS> /cpmd.f:(.text+0xaf6): undefined reference to `genxc_'
VS> /cpmd.f:(.text+0xafd): undefined reference to `numpw_'
VS> /cpmd.f:(.text+0xb2c): undefined reference to `nmr_para_p_'
VS> /cpmd.f:(.text+0xb33): undefined reference to `rinit_'
VS> /cpmd.f:(.text+0xb3a): undefined reference to `rinforce_'
VS> /cpmd.f:(.text+0xb41): undefined reference to `fftprp_'
VS> /cpmd.f:(.text+0xb48): undefined reference to `initclust_'
VS> /cpmd.f:(.text+0xb4f): undefined reference to `dg_init_'
VS> /cpmd.f:(.text+0xb56): undefined reference to `nosalloc_'
VS> /cpmd.f:(.text+0xb5d): undefined reference to `exterp_'
VS> /cpmd.f:(.text+0xb64): undefined reference to `setbasis_'
VS> /cpmd.f:(.text+0xb6b): undefined reference to `dqgalloc_'
VS> /cpmd.f:(.text+0xb72): undefined reference to `setefield_'
VS> /cpmd.f:(.text+0xb7e): undefined reference to `pm_cntl_'
VS> /cpmd.f:(.text+0xb85): undefined reference to `pm_init_'
VS> /cpmd.f:(.text+0xb8e): undefined reference to `pi_cntl_'
VS> /cpmd.f:(.text+0xb95): undefined reference to `pi_init_'
VS> make: *** [cpmd.o] Error 1
VS> 
VS> Vladimir
VS> 
VS> 
VS> ----- Original Message ----- From: "Axel Kohlmeyer"
VS> <akohlmey at cmm.chem.upenn.edu>
VS> To: "oksana ismailova" <o.ismailova at rambler.ru>
VS> Cc: <cpmd-list at cpmd.org>; <pcxcb1 at nottingham.ac.uk>
VS> Sent: Monday, April 07, 2008 6:51 PM
VS> Subject: Re: [CPMD-list] CPMD on 64-bit Linux (openSUSE 10.3) Intel Xeon
VS> 
VS> 
VS> >
VS> > On Mon, 7 Apr 2008, oksana ismailova wrote:
VS> >
VS> > OI> Dear  Axel and  Reuti!
VS> > OI>
VS> > OI>
VS> > OI> Thanks a lot for your  prompt responses and helps.
VS> > OI>
VS> > OI> these options in the Makefile
VS> > OI> worked:
VS> > OI> FFLAGS = -pc64 -O2 -unroll
VS> > OI> LFLAGS = -L/opt/intel/mkl/10.0.2.018/lib/em64t -lmkl_sequential
VS> > OI> -lmkl_lapack
VS> > OI> -lmkl_em64t -lguide lpthread
VS> >
VS> > ok. there is some room for optimization, though.
VS> > the cleaner solution with the best performance would be:
VS> >
VS> > FFLAGS= -O2 -unroll -pc64 -march=pentium3 -mtune=core2
VS> > LFLAGS= -L/opt/intel/mkl/10.0.2.018/lib/em64t -lmkl_intel_lp64
VS> > -lmkl_sequential 
VS> >  -lmkl_core
VS> >
VS> > this will link with the non-openmp version of the libraries
VS> > and thus no -lpthread or -lguide should be needed.
VS> >
VS> > with intel MKL v10 this is required unless you set
VS> > OMP_NUM_THREADS to 1 in your default environment.
VS> >
VS> > additional speedup can be achieved by using FFTW instead of the
VS> > default internal default FFT. for that you'll have to install
VS> > fftw-2 (not fftw3!), change -DFFT_DEFAULT to -DFFT_FFTW and
VS> > add -ldfftw (or -lfftw depending on your Linux) to LFLAGS.
VS> > the major source for the speedup is actually less the speed
VS> > of the FFT different implementations, but the fact that FFTW
VS> > supports more grids, so you may find a smaller grid that
VS> > fits your problem and thus reduces the amount of data to be
VS> > processed (and the memory needed).
VS> >
VS> > cheers,
VS> >   axel.
VS> >
VS> > OI> Based on IFORT-AMD64
VS> > OI>
VS> > OI>
VS> > OI> dear cpmd users,
VS> > OI> any ideas or help will be appreciated
VS> > OI>
VS> > OI> Our system administrator asks  me pass on his thanks also.
VS> > OI>
VS> > OI> best regards,
VS> > OI> oksana
VS> > OI>
VS> > OI>
VS> > OI>
VS> > OI> * cpmd-list-request at cpmd.org [Sat, 05 Apr 2008 05:00:45 +0200]:
VS> > OI> > Send CPMD-list mailing list submissions to
VS> > OI> > cpmd-list at cpmd.org
VS> > OI> >
VS> > OI> > To subscribe or unsubscribe via the World Wide Web, visit
VS> > OI> > http://cpmd.org/mailman/listinfo/cpmd-list
VS> > OI> > or, via email, send a message with subject or body 'help' to
VS> > OI> > cpmd-list-request at cpmd.org
VS> > OI> >
VS> > OI> > You can reach the person managing the list at
VS> > OI> > cpmd-list-owner at cpmd.org
VS> > OI> >
VS> > OI> > When replying, please edit your Subject line so it is more specific
VS> > OI> > than "Re: Contents of CPMD-list digest..."
VS> > OI>
VS> > OI>
VS> > OI> _______________________________________________
VS> > OI> CPMD-list mailing list
VS> > OI> CPMD-list at cpmd.org
VS> > OI> http://cpmd.org/mailman/listinfo/cpmd-list
VS> > OI>
VS> >
VS> > -- 
VS> > =======================================================================
VS> > Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
VS> >   Center for Molecular Modeling   --   University of Pennsylvania
VS> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
VS> > tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
VS> > =======================================================================
VS> > If you make something idiot-proof, the universe creates a better idiot. 
VS> 
VS> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.