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

Mon Apr 28 16:30:12 CET 2008

Axel, everything goes fine if I use

FC = mpif77 -c
LD = mpif77 -i-static

But I actually do not realize why. It compiled ok without these options with 
the 9-th versions of Intel Fortran and MKL.

Sorry for disturbing.

Vladimir

----- Original Message ----- 
From: "Axel Kohlmeyer" <akohlmey at cmm.chem.upenn.edu>
To: "Vladimir Stegailov" <stegailov at ihed.ras.ru>
Cc: <cpmd-list at cpmd.org>
Sent: Monday, April 28, 2008 6:31 PM
Subject: Re: [CPMD-list] CPMD on 64-bit Linux (openSUSE 10.3) Intel Xeon

> 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
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> VS> > OI> >
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> 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
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> specific
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> VS> > OI>
> VS> > OI>
> VS> > OI> _______________________________________________
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> 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. 