[gmx-users] mdrun doesn't run in version 4.0 on sgi server

[Lee Soin]

I try to compile GROMACS with a combination of icc and ifort. Error occurs.
These are the last lines of the compilation message:
Making install in gmx_blas
make[3]: Entering directory
`/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_blas'
make[4]: Entering directory
`/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_blas'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory
`/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_blas'
make[3]: Leaving directory
`/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_blas'
Making install in gmx_lapack
make[3]: Entering directory
`/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_lapack'
make[4]: Entering directory
`/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_lapack'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory
`/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_lapack'
make[3]: Leaving directory
`/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_lapack'
make[3]: Entering directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib'
/bin/sh ../../libtool --tag=CC   --mode=compile
/disk2/junwang/soft/intel/cc/10.1.018/bin/icc -DHAVE_CONFIG_H -I.
-I../../src -I/usr/X11R6/include -I/usr/include/libxml2 -I../../include
-DGMXLIBDIR=\"/disk2/junwang/soft/gromacs4/share/top\"
-I/disk2/junwang/soft/fftw32_mpi/include  -O3 -w -funroll-all-loops -MT
libxdrf.lo -MD -MP -MF .deps/libxdrf.Tpo -c -o libxdrf.lo libxdrf.c
 /disk2/junwang/soft/intel/cc/10.1.018/bin/icc -DHAVE_CONFIG_H -I.
-I../../src -I/usr/X11R6/include -I/usr/include/libxml2 -I../../include
-DGMXLIBDIR=\"/disk2/junwang/soft/gromacs4/share/top\"
-I/disk2/junwang/soft/fftw32_mpi/include -O3 -w -funroll-all-loops -MT
libxdrf.lo -MD -MP -MF .deps/libxdrf.Tpo -c libxdrf.c -o libxdrf.o
libxdrf.c(112): error: identifier "XDR_INT_SIZE" is undefined
        cnt += XDR_INT_SIZE;
               ^
libxdrf.c(140): error: identifier "XDR_INT_SIZE" is undefined
        cnt += XDR_INT_SIZE;
               ^
compilation aborted for libxdrf.c (code 2)
make[3]: *** [libxdrf.lo] Error 1
make[3]: Leaving directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib'
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/disk2/junwang/soft/src/gromacs-4.0/src'
make: *** [install-recursive] Error 1




My intel compiler versions are both 10.1.018.




2008/10/27 Mark Abraham <Mark.Abraham at anu.edu.au>

> Carsten Kutzner wrote:
>
>> Hi,
>>
>> Mark Abraham wrote:
>>
>>> Lee Soin wrote:
>>>
>>>> By invoking "uname -a":
>>>> Linux sgi4700 2.6.16.46-0.12-default #1 SMP Thu May 17 14:00:09 UTC
>>>> 2007 ia64 ia64 ia64 GNU/Linux
>>>>  I don't know any other command to retrieve system information.
>>>>
>>> Hmm, that looks like an SGI Altix 4700. IA64 kernels work on those
>>> machines.
>>>
>> Well, not exactly.
>>
>
> Ah, oops. I was thinking of the Altix 3700 series, which predates
> Montecito. My bad.
>
> They work in combination with Gromacs version <= 3.3.x,
>> but at least I have never managed to get them working with this year's
>> CVS Gromacs or Gromacs 4.x - see also
>>
>> http://www.gromacs.org/pipermail/gmx-developers/2008-February/002405.html
>>
>> The strange thing is that these inner loops have not changed since 3.3.x,
>> so the problem might be somewhere else. But actually the Fortran loops
>> have a quite decent performance on that machine compared to assembly: In
>> a single-CPU test I did with gmx 3.3 they were just about 10% slower.
>>
>
> Good to know. Lee should definitely compare performance when using
> configure with and without --enable-fortran (and using
> --disable-cpu-optimization to avoid needing to set the environment
> variable).
>
>
> Mark
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-- 
Sun Li
Department of Physics
Nanjing University, China
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