Thanks. yes I will try to install this without using cross compiles, and I am doing this on Cray XE6.
Will let you know the results. Thanks you! On Thu, Oct 22, 2015 at 10:19 AM, Szilárd Páll <pall.szil...@gmail.com> wrote: > Please keep the discussion the list! > > There's a lot of information to parse here, I'll do my best, but I'm no > interpreter so I may miss/misread something. :) > > Answers in-line. > > Note that in the GROMACS tool set only mdrun supports MPI, so, while > typically it does not hurt, in general there is no benefit to building > everything with MPI (and there is an mdrun-only target that can be used to > build only mdrun with MPI). > > On Thu, Oct 22, 2015 at 4:46 PM, Ana Marija <sokovic.anamar...@gmail.com> > wrote: > >> 1) if I run it via: >> #!/bin/bash >> #PBS -N test >> #PBS -j oe >> #PBS -l walltime=01:00:00 >> #PBS -l mppwidth=96 >> >> source /opt/modules/default/init/bash >> >> cd $PBS_O_WORKDIR >> module swap PrgEnv-cray PrgEnv-gnu >> #export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH >> #module use /lustre/beagle2/ams/new/modulefiles/ >> #module load plumed/2.2.0 >> export >> LD_LIBRARY_PATH=/lustre/beagle2/gro/gromacs-4.6.7/build/lib:$LD_LIBRARY_PATH >> export LD_LIBRARY_PATH=/opt/fftw/3.3.4.0/abudhabi/lib/:$LD_LIBRARY_PATH >> >> aprun -n 1 -N 1 >> /lustre/beagle2/ams/gro/gromacs-4.6.7/build/bin/grompp_mpi -f >> /lustre/beagle2/ruisun/MYCO/Set-1/input/grompp.mdp -c >> /lustre/beagle2/ruisun/MYCO/Set-1/input/initial.gro -p >> /lustre/beagle2/ruisun/MYCO/Set-1/input/topol.top -n >> /lustre/beagle2/ruisun/MYCO/Set-1/input/index.ndx -o ttmeta1.tpr >> >> .tpr file is never generated instead I am gettig: core file >> and in output file I have this error: >> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# >> _pmiu_daemon(SIGCHLD): [NID 00389] [c7-0c0s2n1] [Wed Oct 21 13:05:44 >> 2015] PE RANK 0 exit signal Segmentation fault >> > > I doubt it's possible to tell why grompp segfaults and how to fix it (not > without a backtrace or repro and further analysis). On our Cray (an XC30 > though) 4.6.7 grompp works fine on the compute nodes (also built with MPI). > > > Other tools do work, I just can't get this input files. >> those sym links are something I have to specify so that those libraries >> can be found on our machine >> > > Note that unless a user does something really exotic, there is little need > for optimized BLAS/LAPACK libs (and there's intermal fallback code), but of > course most of the time linking against libblas/liblapack won't hurt. > > >> I am not sure I understand this: >> "just use CC=gcc CXX=g++ or -DCMAKE_C_COMPILER=$(which gcc) >> -DCMAKE_CXX_COMPILER=$(which g++) to get tools that you can run on the >> login node." >> >> I did: export CC=gcc CXX=g++ >> before running grompp on login nodes via; >> /lustre/beagle2/ams/gro/gromacs-4.6.7/build/bin/grompp_mpi -f >> /lustre/beagle2/ruisun/MYCO/Set-1/input/grompp.mdp -c >> /lustre/beagle2/ruisun/MYCO/Set-1/input/initial.gro -p >> /lustre/beagle2/ruisun/MYCO/Set-1/input/topol.top -n >> /lustre/beagle2/ruisun/MYCO/Set-1/input/index.ndx -o ttmeta1.tpr >> and got Illegal instruction again >> >> so the problem is that I have in my >> /lustre/beagle2/ams/gro/gromacs-4.6.7/build/bin/ only grompp_mpi and that >> can't run on login nodes >> >> did you mean I should do something different? >> > > Yes, I did. You should use the regular C/C++ compiler to build programs > that will run on the login node. So i was suggesting to reconfigure and > compile using > CC=gcc CXX=g++ cmake -DGMX_MPI=OFF [...] && make > Depending on how the login nodes are configured you may also need to tweak > the the instructions enabled, in particular, you _may_ have to > set GMX_USE_RDTSCP=OFF at configure time. > > Let me know how that worked. > > Cheers, > -- > Szilárd > > > >> On Thu, Oct 22, 2015 at 9:31 AM, Szilárd Páll <pall.szil...@gmail.com> >> wrote: >> >>> On Thu, Oct 22, 2015 at 4:27 PM, Ana Marija <sokovic.anamar...@gmail.com >>> > wrote: >>> >>>> if I do that that I got: Illegal Instruction error >>>> which makes sense because I compiled gromacs with cross compiler for >>>> compute nodes >>>> >>> >>> just use CC=gcc CXX=g++ or -DCMAKE_C_COMPILER=$(which gcc) >>> -DCMAKE_CXX_COMPILER=$(which g++) to get tools that you can run on the >>> login node. >>> >>> >>>> >>>> On Thu, Oct 22, 2015 at 9:23 AM, Barnett, James W <jbarn...@tulane.edu> >>>> wrote: >>>> >>>> > On Wed, 2015-10-21 at 10:20 -0500, Ana Marija wrote: >>>> > > Hi, >>>> > > >>>> > > I installed gromacs 4.6.7 with plumed like this: >>>> > > module swap PrgEnv-cray PrgEnv-gnu >>>> > > module load fftw/3.3.4.0 >>>> > > module load cray-mpich/7.0.5 >>>> > > module load gsl/1.15 >>>> > > module load cmake >>>> > > #in /lustre/beagle2/ams/new/gromacs make directory lib2 >>>> > > >>>> > > mkdir lib2 >>>> > > >>>> > > ams@login1:/lustre/beagle2/ams/lib2>ln -s >>>> > > /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a >>>> > > ams@login1:/lustre/beagle2/ams/lib2>ln -s >>>> > > /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a >>>> > > >>>> > > tar zxvf plumed-2.2.0.tgz >>>> > > cd plumed-2.2.0 >>>> > > >>>> > > ./configure CC=cc CXX=CC F77=ftn >>>> > > LDFLAGS="-L/lustre/beagle2/ams/new/gromacs/lib2" >>>> > > --prefix=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0 --enable-mpi >>>> > > --disable-basic-warnings --disable-openmp >>>> > > >>>> > > <strong>###Makefile.conf should look like this, if not please >>>> delete all >>>> > > extra stuff before proceeding to make step</strong> >>>> > > CC=cc >>>> > > FC=gfortran >>>> > > LDF90=gfortran >>>> > > CFLAGS=-g -O2 >>>> > > CXX=CC >>>> > > CXXFLAGS=-O -fPIC >>>> > > CPPFLAGS= -DPACKAGE_NAME=\"PLUMED\" -DPACKAGE_TARNAME=\"plumed\" >>>> > > -DPACKAGE_VERSION=\"2\" -DPACKAGE_STRING=\"PLUMED\ 2\" >>>> > > -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 >>>> > > -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 >>>> > > -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 >>>> > -DHAVE_INTTYPES_H=1 >>>> > > -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_MOLFILE=1 >>>> > > -D__PLUMED_INTERNAL_MOLFILE_PLUGINS=1 -D__PLUMED_MPI=1 >>>> > > -D__PLUMED_HAS_CLOCK_GETTIME=1 -D__PLUMED_HAS_GETTIMEOFDAY=1 >>>> > > -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 >>>> -D__PLUMED_HAS_EXECINFO=1 >>>> > > -D__PLUMED_HAS_ZLIB=1 -DNDEBUG=1 -D_REENTRANT=1 >>>> > > LDFLAGS= >>>> > > DYNAMIC_LIBS=-lstdc++ -lz -ldl -L/lustre/beagle2/ams/groplu/lib2 >>>> > > LIBS=-ldl >>>> > > SOEXT= >>>> > > LD=CC >>>> > > LDSO=CC -shared >>>> > > GCCDEP=CC >>>> > > prefix=/lustre/beagle2/ams/groplu/plumed-2.1.1 >>>> > > ### >>>> > > >>>> > > make >>>> > > make install >>>> > > >>>> > > export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH >>>> > > >>>> > > #1. Make a directory for modulefiles (e.g. >>>> > > /lustre/beagle2/ams/new/modulefiles/) >>>> > > #2. Copy file: cp >>>> > > /lustre/beagle2/ams/new/gromacs/plumed-2.2.0/lib/plumed/modulefile >>>> > > /lustre/beagle2/ams/new/modulefiles/plumed/2.2.0/ >>>> > > #3. type "module use /lustre/beagle2/ams/new/modulefiles/" >>>> > > #4. type "module load plumed/2.2.0" >>>> > > >>>> > > export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH >>>> > > module use /lustre/beagle2/ams/new/modulefiles/ >>>> > > module load plumed/2.2.0 >>>> > > >>>> > > ### instal gromacs 4.6.7 >>>> > > wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.7.tar.gz >>>> > > tar zxvf gromacs-4.6.7.tar.gz >>>> > > cd gromacs-4.6.7/ >>>> > > ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-4.6.7>plumed-patch >>>> -p >>>> > > --static >>>> > > >>>> > > >>>> > > PLUMED patching tool >>>> > > >>>> > > 1) amber14 3) gromacs-4.6.7 5) lammps-6Apr13 7) >>>> namd-2.9 >>>> > > 2) gromacs-4.5.5 4) gromacs-5.0 6) namd-2.8 8) >>>> > qespresso-5.0.2 >>>> > > >>>> > > Choose the best matching code/version:3 >>>> > > >>>> > > mkdir build >>>> > > cd build >>>> > > >>>> > > >>>> > > export BUILD_WITH_INSTALL_RPATH=TRUE >>>> > > export INSTALL_RPATH="" >>>> > > export SKIP_BUILD_RPATH=TRUE >>>> > > export >>>> > > >>>> > >>>> CMAKE_LIBRARY_PATH="/lustre/beagle2/ams/new/gromacs/lib:$CMAKE_LIBRARY_PATH" >>>> > > >>>> > > #in /lustre/beagle2/ams/new/gromacs make directory lib >>>> > > >>>> > > ams@login1:/lustre/beagle2/ams/new/gromacs/lib>ln -s >>>> > > /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a >>>> > > ams@login1:/lustre/beagle2/ams/new/gromacs/lib>ln -s >>>> > > /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a >>>> > > >>>> > > >>>> > > cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include >>>> > > -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a >>>> > > -DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2- >>>> > > gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2- >>>> > > gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2- >>>> > > >>>> > >>>> gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default >>>> > > >>>> > >>>> /lib64/librca.a;/opt/gcc/4.9.1/snos/lib64/libgfortran.a;/opt/gcc/4.9.1/snos/li >>>> > > >>>> > >>>> b64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/defau >>>> > > >>>> > >>>> lt/lib64/libalpsutil.a;/opt/gcc/4.9.1/snos/lib64/libgomp.a;/opt/gcc/4.9.1/snos >>>> > > >>>> > >>>> /lib64/libquadmath.a;/opt/cray/ugni/default/lib64/libugni.a;/opt/cray/udreg/de >>>> > > >>>> > >>>> fault/lib64/libudreg.a;/opt/cray/xpmem/default/lib64/libxpmem.a;/opt/cray/wlm_ >>>> > > detect/default/lib64/libwlm_detect.a;/lib64/libdl.so.2" >>>> > > -DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include" >>>> > > -DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_FORCE_CXX=ON >>>> > > -DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF >>>> -DGMX_MPI=ON >>>> > > >>>> > >>>> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/new/gromacs/gromacs-4.6.7/build >>>> > > -DGMX_X11=OFF >>>> > -DGMX_BLAS_USER=/lustre/beagle2/ams/new/gromacs/lib/libblas.a >>>> > > -DGMX_LAPACK_USER=/lustre/beagle2/ams/new/gromacs/lib/liblapack.a >>>> > > -DCMAKE_SKIP_RPATH=ON >>>> > > >>>> > > >>>> > > make >>>> > > make install >>>> > > >>>> > > I am getting Segmentation error if I run it like this: >>>> > > >>>> > > #!/bin/bash >>>> > > #PBS -N test >>>> > > #PBS -j oe >>>> > > #PBS -l walltime=01:00:00 >>>> > > #PBS -l mppwidth=96 >>>> > > >>>> > > source /opt/modules/default/init/bash >>>> > > >>>> > > cd $PBS_O_WORKDIR >>>> > > module swap PrgEnv-cray PrgEnv-gnu >>>> > > export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH >>>> > > module use /lustre/beagle2/ams/new/modulefiles/ >>>> > > module load plumed/2.2.0 >>>> > > export >>>> > > LD_LIBRARY_PATH=/lustre/beagle2/ams/new/gromacs/gromacs- >>>> > > 4.6.7/build/lib:$LD_LIBRARY_PATH >>>> > > export LD_LIBRARY_PATH=/opt/fftw/ >>>> 3.3.4.0/abudhabi/lib/:$LD_LIBRARY_PATH >>>> > > >>>> > > aprun -n 1 -N 1 >>>> > > /lustre/beagle2/gro/gromacs/gromacs-4.6.7/build/bin/grompp_mpi -f >>>> > > /lustre/beagle2/ruisun/MYCO/Set-1/input/grompp.mdp -c >>>> > > /lustre/beagle2/ruisun/MYCO/Set-1/input/initial.gro -p >>>> > > /lustre/beagle2/ruisun/MYCO/Set-1/input/topol.top -n >>>> > > /lustre/beagle2/ruisun/MYCO/Set-1/input/index.ndx -o ttmeta1.tpr >>>> > > >>>> > > The same error happens if I install gromacs without plumed. >>>> > >>>> > So it's not an issue with plumed. >>>> > >>>> > > >>>> > > Can somebody please advise me what to do here? >>>> > >>>> > Have you tried running grompp without using aprun (you would benefit >>>> doing >>>> > this >>>> > in an interactive session to see the output right away)? >>>> > >>>> > > >>>> > > Thanks >>>> > > Ana >>>> > >>>> > >>>> > >>>> > -- >>>> > James "Wes" Barnett, Ph.D. Candidate >>>> > Louisiana Board of Regents Fellow >>>> > >>>> > Chemical and Biomolecular Engineering >>>> > Tulane University >>>> > 341-B Lindy Boggs Center for Energy and Biotechnology >>>> > 6823 St. Charles Ave >>>> > New Orleans, Louisiana 70118-5674 >>>> > jbarn...@tulane.edu >>>> > -- >>>> > Gromacs Users mailing list >>>> > >>>> > * Please search the archive at >>>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> > posting! >>>> > >>>> > * Can't post? 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