[gmx-users] failure during compiling gromacs 4.5.5

Szilárd Páll szilard.pall at cbr.su.se
Tue Oct 25 21:16:13 CEST 2011


> Thank you very much. I removed -xHOST from CFLAGS and FFLAGS, and now it
> runs correctly.

Good that it worked. Still it's bizarre that icc failed at compiling
the code it generated...

FYI: removing the flag might result in slightly slower binaries, but
the difference should be quite small, I guess at most 2-3%.

> As for Intel Compile 2011 sp1 + openmpi on my cluster, mpif90 and mpicc
> give "segmentation fault" error message.

Whooops, that's not good. As it could be anything from an incorrectly
configured OpenMPI to buggy Gromacs build scripts, unless you want to
investigate the issue I'd say let's do not worry about that now. :)


> Best regards,
> Ye
> 2011-10-25
> ________________________________
> From: Szil醨d P醠l
> Date: 2011-10-25  03:42:17
> To: Discussion list for GROMACS users
> CC:
> Subject: Re: [gmx-users] failure during compiling gromacs 4.5.5
> Hi,
> The error messages are all referring to SSE 4.1 packed integer min/max
> operations not being recognized. I assume that these were enabled by
> the "-xHOST" compiler option, and icc automatically generated these
> instructions - the files it's complaining about are even temporary
> files.
> Could it be that you have a broken installation of Intel Compilers on
> your cluster? You could check if it works if you remove -xHOST or
> explicitly state -xSSE4.1.
> Just for curiosity, what are the issues with the Intel Compiler 2011
> (I assume that's 12.x) + OpenMPI?
> Cheers,
> --
> Szilárd
> On Mon, Oct 24, 2011 at 4:53 PM, Ye MEI <ymei at itcs.ecnu.edu.cn> wrote:
>> Dear Gromacs users,
>> I am trying to install gromacs on my cluster using Intel Compiler 11.1.072
>> and FFTW3. But I met the following error message
>>  icc -DHAVE_CONFIG_H -I. -I../../../src -I/usr/include/libxml2 -I../../../include -I/usr/local/include -xHOST -I/home/users/ymei/software/fftw3/intel/include -pthread -I./include -MT type.lo -MD -MP -MF .deps/type.Tpo -c type.c -o type.o
>> /tmp/iccLPSVQqas_.s: Assembler messages:
>> /tmp/iccLPSVQqas_.s:92: Error: no such instruction: `pmaxsb %xmm0,%xmm1'
>> /tmp/iccLPSVQqas_.s:100: Error: no such instruction: `pmaxsb (%r8,%rdx),%xmm0'
>> /tmp/iccLPSVQqas_.s:228: Error: no such instruction: `pminsb %xmm0,%xmm1'
>> /tmp/iccLPSVQqas_.s:236: Error: no such instruction: `pminsb (%r8,%rdx),%xmm0'
>> /tmp/iccLPSVQqas_.s:2559: Error: no such instruction: `pmaxsd %xmm0,%xmm1'
>> /tmp/iccLPSVQqas_.s:2567: Error: no such instruction: `pmaxsd (%rdx,%r9,4),%xmm0'
>> /tmp/iccLPSVQqas_.s:2709: Error: no such instruction: `pminsd %xmm0,%xmm1'
>> /tmp/iccLPSVQqas_.s:2717: Error: no such instruction: `pminsd (%rdx,%r9,4),%xmm0'
>> /tmp/iccLPSVQqas_.s:2989: Error: no such instruction: `pmulld %xmm0,%xmm1'
>> /tmp/iccLPSVQqas_.s:2997: Error: no such instruction: `pmulld (%rdx,%rax,4),%xmm0'
>> /tmp/iccLPSVQqas_.s:7009: Error: no such instruction: `pmaxsb %xmm0,%xmm1'
>> /tmp/iccLPSVQqas_.s:7017: Error: no such instruction: `pmaxsb (%r8,%rdx),%xmm0'
>> /tmp/iccLPSVQqas_.s:7145: Error: no such instruction: `pminsb %xmm0,%xmm1'
>> /tmp/iccLPSVQqas_.s:7153: Error: no such instruction: `pminsb (%r8,%rdx),%xmm0'
>> /tmp/iccLPSVQqas_.s:9313: Error: no such instruction: `pmaxuw %xmm0,%xmm1'
>> /tmp/iccLPSVQqas_.s:9321: Error: no such instruction: `pmaxuw (%rdx,%r9,2),%xmm0'
>> /tmp/iccLPSVQqas_.s:9463: Error: no such instruction: `pminuw %xmm0,%xmm1'
>> /tmp/iccLPSVQqas_.s:9471: Error: no such instruction: `pminuw (%rdx,%r9,2),%xmm0'
>> /tmp/iccLPSVQqas_.s:10621: Error: no such instruction: `pmaxud %xmm0,%xmm1'
>> /tmp/iccLPSVQqas_.s:10629: Error: no such instruction: `pmaxud (%rdx,%r9,4),%xmm0'
>> /tmp/iccLPSVQqas_.s:10771: Error: no such instruction: `pminud %xmm0,%xmm1'
>> /tmp/iccLPSVQqas_.s:10779: Error: no such instruction: `pminud (%rdx,%r9,4),%xmm0'
>> /tmp/iccLPSVQqas_.s:11051: Error: no such instruction: `pmulld %xmm0,%xmm1'
>> /tmp/iccLPSVQqas_.s:11059: Error: no such instruction: `pmulld (%rdx,%rax,4),%xmm0'
>> /tmp/iccLPSVQqas_.s:15514: Error: no such instruction: `pmaxsb %xmm0,%xmm1'
>> /tmp/iccLPSVQqas_.s:15522: Error: no such instruction: `pmaxsb (%r8,%rdx),%xmm0'
>> /tmp/iccLPSVQqas_.s:15650: Error: no such instruction: `pminsb %xmm0,%xmm1'
>> /tmp/iccLPSVQqas_.s:15658: Error: no such instruction: `pminsb (%r8,%rdx),%xmm0'
>> make[4]: *** [type.lo] Error 1
>> make[4]: Leaving directory `/home/users/ymei/software/gromacs-4.5.5/src/gmxlib/thread_mpi'
>> make[3]: *** [all-recursive] Error 1
>> make[3]: Leaving directory `/home/users/ymei/software/gromacs-4.5.5/src/gmxlib'
>> make[2]: *** [all-recursive] Error 1
>> make[2]: Leaving directory `/home/users/ymei/software/gromacs-4.5.5/src'
>> make[1]: *** [all] Error 2
>> make[1]: Leaving directory `/home/users/ymei/software/gromacs-4.5.5/src'
>> make: *** [all-recursive] Error 1
>> I have never seen this kind of error message before, and I donot know what
>> to do to solve this problem. Can anyone help me out?
>> Intel Compiler 2011 is ok. But this version does not work well with my
>> cluster, especially with openmpi.
>> And the following information might be helpful.
>> ymei at CLOUD@ECNU:~/software/gromacs-4.5.5> gcc -v
>> Using built-in specs.
>> Target: x86_64-suse-linux
>> Configured with: ../configure --enable-threads=posix --prefix=/usr --with-local-prefix=/usr/local --infodir=/usr/share/info --mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 --enable-languages=c,c++,objc,fortran,obj-c++,java,ada --enable-checking=release --with-gxx-include-dir=/usr/include/c++/4.1.2 --enable-ssp --disable-libssp --disable-libgcj --with-slibdir=/lib64 --with-system-zlib --enable-shared --enable-__cxa_atexit --enable-libstdcxx-allocator=new --program-suffix= --enable-version-specific-runtime-libs --without-system-libunwind --with-cpu=generic --host=x86_64-suse-linux
>> Thread model: posix
>> gcc version 4.1.2 20070115 (SUSE Linux)
>> ymei at CLOUD@ECNU:~/software/gromacs-4.5.5> cat /etc/SuSE-release
>> SUSE Linux Enterprise Server 10 (x86_64)
>> VERSION = 10
>> Thank you in advance.
>> Ye
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

More information about the gromacs.org_gmx-users mailing list