[gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Ana Marija sokovic.anamarija at gmail.com
Thu Oct 22 17:23:23 CEST 2015 

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.szilard at 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.anamarija at 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.szilard at gmail.com>
>> wrote:
>>
>>> On Thu, Oct 22, 2015 at 4:27 PM, Ana Marija <sokovic.anamarija at 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 <jbarnet4 at 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 at login1:/lustre/beagle2/ams/lib2>ln -s
>>>> > > /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
>>>> > > ams at 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 at 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 at 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 at 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
>>>> > jbarnet4 at tulane.edu
>>>> > --
>>>> > Gromacs Users mailing list
>>>> >
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>>>
>>>
>>
>

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