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? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.