[gmx-users] Benching against different compilers - Help needed

David van der Spoel spoel at xray.bmc.uu.se
Sun Apr 30 22:35:51 CEST 2006


Jones de Andrade wrote:
> Hi All.
> 
> Well, first of all, I would like to thank a lot David for all the help 
> he gave me up to now. I don't know how to thank for so much help neither 
> how to apologize for bothering you this much.
> 
> Up to now, I could finally compile it with Portland, in both single and 
> double precision version. But, on the other hand, while the single 
> precision works properly, the double precision fails in some tests, like 
> the "mixed" test on the "tutor" directory. It yelds me the following 
> error message:
> 

this is hard to debug, but what you could do is run the same tpr with 
different executables and do gmxcheck -e -e2 to compare energies. that 
might give a clue.

> _________________________________________________________________________
> starting mdrun 'Pure Methanol - Yummie! (and some water)'
> 10000 steps,     20.0 ps.
> 
> 
> Back Off! I just backed up traj.trr to ./#traj.trr.10#
> 
> Back Off! I just backed up traj.xtc to ./#traj.xtc.10#
> step 0
> Step 1  Warning: pressure scaling more than 1%, mu: 1.01018 1.02193 1.08117
> 
> Step 2  Warning: pressure scaling more than 1%, mu: 1.01124 1.00787 1.08362
> 
> Step 3  Warning: pressure scaling more than 1%, mu: 1.03039 1.0523 1.08046
> 
> Step 4  Warning: pressure scaling more than 1%, mu: 1.04141 1.08638 1.09351
> 
> Step 5  Warning: pressure scaling more than 1%, mu: 1.06415 1.0995 1.06772
> 
> Step 6  Warning: pressure scaling more than 1%, mu: 1.04802 1.07721 1.04162
> 
> Step 7  Warning: pressure scaling more than 1%, mu: 1.02981 1.03652 1.01836
> 
> Step 8  Warning: pressure scaling more than 1%, mu: 1.01626 1.01848 1.00881
> 
> Step 9  Warning: pressure scaling more than 1%, mu: 1.01081 1.01178 1.00552
> step 130, remaining runtime:     0 s
> Step 140  Warning: pressure scaling more than 1%, mu: 1.00411 1.00022 1.0102
> step 140, remaining runtime:     0 s
> Step 141  Warning: pressure scaling more than 1%, mu: 1.00439 1.00019 
> 1.01173
> 
> Step 142  Warning: pressure scaling more than 1%, mu: 1.00395 1.00019 
> 1.01172
> 
> Step 143  Warning: pressure scaling more than 1%, mu: 1.00304 1.00017 
> 1.01009
> step 240, remaining runtime:    40 s               
> -------------------------------------------------------
> Program mdrun_d, VERSION 3.3
> Source code file: stat.c, line: 283
> 
> Fatal error:
> XTC error
> -------------------------------------------------------
> 
> "May the Force Be With You" (Star Wars)
> ___________________________________________________________________________
> 
> 
> By the way: this test runs properly and without any error in both 
> (single and double precision) compilations with GCC, and in the single 
> precision compilation with Portland.  :(
> 
> Does anybody have any idea of this kind of error? Is it a known issue, 
> someone has came across this kind of behavior before?
> 
> Thanks a lot everybody for all and any help in advance! ;)
> 
> Jones
> 
> On 4/27/06, *David van der Spoel* <spoel at xray.bmc.uu.se 
> <mailto:spoel at xray.bmc.uu.se>> wrote:
> 
>     Jones de Andrade wrote:
>      > Hi.
>      >
>      > Sorry if it looks like a stupidy question (and it is), but I'm
>     quite bad
>      > on C (fortran addicted).
>      >
>      > I found 4 entries in the file like the one you told me to change.
>     May I
>      > change all them, or which ones?
>      >
>     only the one in the function that the compiler complains about. goto
>     line 313 and then upwards from there until you find the offensive
>     declaration.
> 
>      > Thanks a lot,
>      >
>      > Jones
>      >
>      > On 4/26/06, *David van der Spoel* <spoel at xray.bmc.uu.se
>     <mailto:spoel at xray.bmc.uu.se>
>      > <mailto:spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se> >> wrote:
>      >
>      >     Jones de Andrade wrote:
>      >      > Hi all.
>      >      >
>      >      > Well, some time ago I decided to bench gromacs on AMD64
>     machines
>      >      > compiled with different compilers (both single and double
>     precision,
>      >      > both internal and external blas and lapack, just FFTw 3
>     for fourier)
>      >      > in order to see which one performs better.
>      >      >
>      >      > To time, I have available GCC, PGI and Intel compilers.
>     Pathscale
>      >     is a
>      >      > future option.
>      >      >
>      >      > Unfortunatelly, I was able to properly compile it just
>     with GCC
>      >     (all 4
>      >      > flavours, despite the fact that the external libraries of
>     ACML didn't
>      >      > seem to improve so much the performance as I expected),
>     but failed on
>      >      > both PGI and Intel compilers at different points. So, I'm
>     asking for
>      >      > help on those compilation issues.
>      >      >
>      >      > For Intel, the compilation ends up with a segmentation
>     fault at the
>      >      > following point:
>      >      >
>      >      >
>      >    
>     ***********************************************************************************
> 
>      >
>      >      > ./mknb   -software_invsqrt
>      >      >  >>> Gromacs nonbonded kernel generator (-h for help)
>      >      >  >>> Generating single precision functions in C.
>      >      >  >>> Using Gromacs software version of 1/sqrt(x).
>      >      >  make[5]: *** [kernel-stamp] Falha de segmentação
>      >      >  make[5]: Leaving directory
>      >      >
>      >    
>     `/home/johannes/src/gromacs/gromacs-3.3/src/gmxlib/nonbonded/nb_kernel'
>      >      >  make[4]: ** [all-recursive] Erro 1
>      >      >
>      >    
>     ***********************************************************************************
>      >      >
>      >      > And, for PGI, it dies at the following point (after using the
>      >      > --without-x --without-motif-libraries --
>     without-motif-includes
>      >     flags
>      >      > for configure):
>      >      >
>      >      >
>      >    
>     ****************************************************************************************
>      >      > source='gmx_sgangle.c' object='gmx_sgangle.lo' libtool=yes \
>      >      >  DEPDIR=.deps depmode=none /bin/sh ../../config/depcomp \
>      >      >  /bin/sh ../../libtool --mode=compile --tag=CC
>      >      > /usr/local/pgi/linux86-64/6.0/bin/pgcc -DHAVE_CONFIG_H -I.
>     -I.
>      >      > -I../../src  -I../../include
>      >      >
>     -DGMXLIBDIR=\"/usr/local/bin/chemistry/gromacs/PSI//share/top\"
>      >      > -I/usr/local/lib64/fftw/pgi/include  -tp=k8-64 -fastsse
>     -Mipa=fast
>      >      > -Mipa=inline -c -o gmx_sgangle.lo gmx_sgangle.c
>      >      >   /usr/local/pgi/linux86-64/6.0/bin/pgcc -DHAVE_CONFIG_H
>     -I. -I.
>      >      > -I../../src -I../../include
>      >      >
>     -DGMXLIBDIR=\"/usr/local/bin/chemistry/gromacs/PSI//share/top\"
>      >      > -I/usr/local/lib64/fftw/pgi/include -tp=k8-64 -fastsse
>     -Mipa=fast
>      >      > -Mipa=inline -c gmx_sgangle.c -o gmx_sgangle.o
>      >      >  PGC-S-0090-Scalar data type required for logical expression
>      >      > (gmx_sgangle.c: 313)
>      >      >  PGC-S-0090-Scalar data type required for logical expression
>      >      > (gmx_sgangle.c: 320)
>      >      >  PGC/x86-64 Linux/x86-64 6.0-5: compilation completed with
>     severe
>      >     errors
>      >      >
>      >    
>     **************************************************************************************
>      >
>      >      >
>      >     Shitty compiler...
>      >
>      >     replace in the header of the function
>      >     matrix box,
>      >     by
>      >     rvec *box
>      >
>      >
>      >      > Did anyone run into those problems before when trying to
>     compile
>      >      > gromacs with those compilers?
>      >      >
>      >      > Any help will be very welcome. :)
>      >      >
>      >      > Thanks a lot in advance,
>      >      >
>      >      > Jones
>      >      >
>      >      > P.S.: I'm using the "mixed" run simulation of the "tutor"
>      >     directory as
>      >      > a compilation test.
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>      >
>      >     --
>      >     David.
>      >    
>     ________________________________________________________________________
>      >
>      >     David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics
>     group,
>      >     Dept. of Cell and Molecular Biology, Uppsala University.
>      >     Husargatan 3, Box 596,          75124 Uppsala, Sweden
>      >     phone:  46 18 471 4205          fax: 46 18 511 755
>      >     spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>      >     <mailto:spoel at xray.bmc.uu.se
>     <mailto:spoel at xray.bmc.uu.se>>    spoel at gromacs.org
>     <mailto:spoel at gromacs.org>
>      >     <mailto:spoel at gromacs.org <mailto:spoel at gromacs.org>>  
>     http://folding.bmc.uu.se
>      >    
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> 
>     --
>     David.
>     ________________________________________________________________________
>     David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>     Dept. of Cell and Molecular Biology, Uppsala University.
>     Husargatan 3, Box 596,          75124 Uppsala, Sweden
>     phone:  46 18 471 4205          fax: 46 18 511 755
>     spoel at xray.bmc.uu.se
>     <mailto:spoel at xray.bmc.uu.se>    spoel at gromacs.org
>     <mailto:spoel at gromacs.org>   http://folding.bmc.uu.se
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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