Re: [gmx-users] New maintenance release: gromacs-4.5.4
Thank you for the new version of gromacs. But the compilation of gromacs failed on my computer. The commands are as follows: make distclean export CC=icc export F77=ifort export CXX=icc export CFLAGS="-xS -I/apps/fftw3/include" export FFLAGS="-xS -I/apps/fftw3/include" export CXXFLAGS="-I/apps/fftw3/include" export LDFLAGS="-L/apps/fftw3/lib -lfftw3f" ./configure --prefix=/apps/gromacs4.5 --with-fft=fftw3 --with-x --with-qmmm-gaussian make and the error message is icc -shared .libs/calcmu.o .libs/calcvir.o .libs/constr.o .libs/coupling.o .libs/domdec.o .libs/domdec_box.o .libs/domdec_con.o .libs/domdec_network.o .libs/domdec_setup.o .libs/domdec_top.o .libs/ebin.o .libs/edsam.o .libs/ewald.o .libs/force.o .libs/forcerec.o .libs/ghat.o .libs/init.o .libs/mdatom.o .libs/mdebin.o .libs/minimize.o .libs/mvxvf.o .libs/ns.o .libs/nsgrid.o .libs/perf_est.o .libs/genborn.o .libs/genborn_sse2_single.o .libs/genborn_sse2_double.o .libs/genborn_allvsall.o .libs/genborn_allvsall_sse2_single.o .libs/genborn_allvsall_sse2_double.o .libs/gmx_qhop_parm.o .libs/gmx_qhop_xml.o .libs/groupcoord.o .libs/pme.o .libs/pme_pp.o .libs/pppm.o .libs/partdec.o .libs/pull.o .libs/pullutil.o .libs/rf_util.o .libs/shakef.o .libs/sim_util.o .libs/shellfc.o .libs/stat.o .libs/tables.o .libs/tgroup.o .libs/tpi.o .libs/update.o .libs/vcm.o .libs/vsite.o .libs/wall.o .libs/wnblist.o .libs/csettle.o .libs/clincs.o .libs/qmmm.o .libs/gmx_fft.o .libs/gmx_parallel_3dfft.o .libs/fft5d.o .libs/gmx_wallcycle.o .libs/qm_gaussian.o .libs/qm_mopac.o .libs/qm_gamess.o .libs/gmx_fft_fftw2.o .libs/gmx_fft_fftw3.o .libs/gmx_fft_fftpack.o .libs/gmx_fft_mkl.o .libs/qm_orca.o .libs/mdebin_bar.o -Wl,--rpath -Wl,/home/ymei/gromacs-4.5.4/src/gmxlib/.libs -Wl,--rpath -Wl,/apps/gromacs4.5/lib -lxml2 -L/apps/fftw3/lib /apps/fftw3/lib/libfftw3f.a ../gmxlib/.libs/libgmx.so -lnsl -pthread -Wl,-soname -Wl,libmd.so.6 -o .libs/libmd.so.6.0.0 ld: /apps/fftw3/lib/libfftw3f.a(problem.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /apps/fftw3/lib/libfftw3f.a: could not read symbols: Bad value However, it works fine for gromacs 4.5.3. Can anyone help? Ye MEI 2011-03-22 From： Rossen Apostolov Date： 2011-03-22 03:24:55 To： Discussion list for GROMACS development; Discussion list for GROMACS users; gmx-announce CC： Subject： [gmx-users] New maintenance release: gromacs-4.5.4 Dear Gromacs community, A new maintenance release of Gromacs is available for download at ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.4.tar.gz. Some notable updates in this release: * Fixed pdb2gmx picking up force field from local instead of library directory * Made pdb2gmx vsite generation work again for certain His namings. * Fixed incorrect virial and pressure averages with certain nst... values (instantaneous values correct) * Fixed incorrect cosine viscosity output * New -multidir alternative for mdrun -multi option * Several minor fixes in analysis tools * Several updates to the program documentation Big thanks to all developers and users! Happy simulating! Rossen -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] failure during compiling gromacs 4.5.5
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@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@CLOUD@ECNU:~/software/gromacs-4.5.5> cat /etc/SuSE-release SUSE Linux Enterprise Server 10 (x86_64) VERSION = 10 PATCHLEVEL = 2 Thank you in advance. Ye -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Re: [gmx-users] failure during compiling gromacs 4.5.5
Dear Szilárd， Thank you very much. I removed -xHOST from CFLAGS and FFLAGS, and now it runs correctly. As for Intel Compile 2011 sp1 + openmpi on my cluster, mpif90 and mpicc give "segmentation fault" error message. 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 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@CLOUD@ECNU:~/software/g
Re: [gmx-users] Cuda not detected
try nvidia-smi -a to see whether the GPU card has been correctly configured. This happens on my GPU node. Every time I reboot the computer, I must reconfigure the GPU cards with "nvidia-smi -a" using root account. Ye 2011-11-17 From： Andrzej Rzepiela Date： 2011-11-17 21:01:07 To： gmx-users CC： Subject： [gmx-users] Cuda not detected Hey, I am playing with the gpu version of mdrun and could make it run with: ~/gromacs/gpu/bin/mdrun-gpu -s topol.tpr -device "OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes" However after reboot of the machine ( which is a testing machine) I get the following error: --- Program mdrun-gpu, VERSION 4.5.5 Source code file: /home/weber/gromacs/gromacs-4.5.5_gpu/src/kernel/ openmm_wrapper.cpp, line: 1272 Fatal error: The requested platform "Cuda" could not be found. echo $LD_LIBRARY_PATH:/opt/software/ganglia-3.1.7/lib64:/opt/software/ htop-0.8.3:/usr/local/cuda/lib64:/usr/local/cuda/lib:/home/weber/ OpenMM3.1.1-Linux64/lib echo $PATH/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/usr/games:/usr/ lib64/jvm/jre/bin:/opt/software/nvidia/3.2.16/cuda/bin:/opt/software/ ganglia-3.1.7/bin:/opt/software/htop-0.8.3/bin:/usr/lib/mit/bin:/usr/ lib/mit/sbin:.:/usr/local/cuda/bin:/home/weber/cmake-2.8.6/bin I run a simple gpu test program and it works. I believe something is not linked correctly, maybe someone can give me a hint. Thank You Andrzej -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] QM/MM tutorial available?
Dear Gromacs users, Is there any QM/MM tutorials for gromacs 3.3.3 or 4.0.5 available on line? I cannot find any tutorials that run smoothly with either 3.3.3 or 4.0.5. Thank you in advance. Ye MEI ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] a bug in GMXRC.bash
Dear Gromacs developers, I noticed that the GMXRC.bash has been updated in gromacs 4.5.2, which leads to a wrong manipulation to the LD_LIBRARY_PATH variable. The leading colon is missing, when exporting this variable for the first time. 2010-11-08 Ye MEI -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Re: [gmx-users] a bug in GMXRC.bash
But later LD_LIBRARY_PATH is redefined as
LD_LIBRARY_PATH=${GMXLDLIB}${LD_LIBRARY_PATH}
without a colon between ${GMXLDLIB} and ${LD_LIBRARY_PATH}
Ye MEI
2010-11-08
From: Roland Schulz
Date: 2010-11-08 15:31:24
To: Discussion list for GROMACS users
CC:
Subject: Re: [gmx-users] a bug in GMXRC.bash
This was removed for security reasons. The leading colon adds the local
directory to the list of directories searched for libraries. Why does your
setup require the colon?
Roland
On Mon, Nov 8, 2010 at 2:04 AM, Ye MEI wrote:
Dear Gromacs developers,
I noticed that the GMXRC.bash has been updated in gromacs 4.5.2, which leads to
a wrong manipulation to the LD_LIBRARY_PATH variable.
The leading colon is missing, when exporting this variable for the first time.
2010-11-08
Ye MEI
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[gmx-users] question about simualtion of CNT from a rookie
Dear all, I am trying to study an infinite length CNT in SPC water box under NPT using gromacs 4.5.3. The axis of CNT is along Z direction. The options "pbc = xyz " and "periodic_molecules = yes" are included in all mdp files. The whole system was minimized first, followed by an NVT simulation. The structure was fine, at least when visualized with VMD. Then I ran an NPT simulation with weak restraint on CNT. The pressure coupling options are set as following ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of box vectors tau_p = 2.0 0.0 ; time constant, in ps ref_p = 1.0 0.0 ; reference pressure, in bar compressibility = 4.5e-5 0.0; isothermal compressibility of water, bar^-1 And the final structure was also fine. But then I removed the constraint, and tried to run a long time simulation under NPT, the whole system exploded in several ps. I have not figured out what was wrong in my calculation. Can anyone give me a suggestion? Ye MEI -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
