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

David van der Spoel Sun, 30 Apr 2006 13:44:25 -0700

Jones de Andrade wrote:

Hi All.
Well, first of all, I would like to thank a lot David for all the helphe gave me up to now. I don't know how to thank for so much help neitherhow to apologize for bothering you this much.
Up to now, I could finally compile it with Portland, in both single anddouble precision version. But, on the other hand, while the singleprecision works properly, the double precision fails in some tests, likethe "mixed" test on the "tutor" directory. It yelds me the followingerror message:

this is hard to debug, but what you could do is run the same tpr withdifferent executables and do gmxcheck -e -e2 to compare energies. thatmight 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 1.000191.01173

Step 142 Warning: pressure scaling more than 1%, mu: 1.00395 1.000191.01172

Step 143 Warning: pressure scaling more than 1%, mu: 1.00304 1.000171.01009step 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 singleprecision 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* <[EMAIL PROTECTED]<mailto:[EMAIL PROTECTED]>> 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* <[EMAIL PROTECTED]
    <mailto:[EMAIL PROTECTED]>
     > <mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> >> 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
     >     [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
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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
    [EMAIL PROTECTED]
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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
[EMAIL PROTECTED]       [EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re: [gmx-users] Benching against different compilers - Help needed

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