[gmx-users] Gromacs 4.6.7 plumed /segmentation error with imput files

Fri Oct 16 18:00:48 CEST 2015

Hi,

Please keep the discussion on the list. Someone else may have this problem
some time.

On Fri, Oct 16, 2015 at 5:51 PM Ana Marija <sokovic.anamarija at gmail.com>
wrote:

> HI Mark,
>
> but I do use cross compiler flags like: -DCMAKE_CXX_COMPILER=CC
> -DCMAKE_C_COMPILER=cc
> because yes I want to run it on compute nodes.
>

You still need the right modules loaded at cmake, build and run time. You
should ask your sysadmins to help you install a normal gromacs 4.6.7, and
then steal their ideas ;-)

> Also I'm using cross compiler flags for plumed. Is there is another thing
> I can change there?
>

No idea, but you should ask them. :-)

> Also you are saying that I shouldn't use imput files generated with 4.5.5
> with 4.6.7?
>

You should prefer to use grompp that matches the mdrun, and you should not
run grompp on the compute nodes at all! That's why grompp produces a fully
portable standalone .tpr.

Mark

>
> Thanks
> Ana
>
> On Fri, Oct 16, 2015 at 10:45 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> 4.6.7 is fine, but you are probably having trouble with the fact that
>> your login node is a different kind of machine from your compute node, and
>> you'll need to consult your local docs for how to set up the cross
>> compilation environment to work correctly (and then how to tell PLUMED
>> about it). There's generally no reason to want to run grompp on the compute
>> nodes, nor mdrun on the login nodes, but if I'm right then the way they've
>> designed your infrastructure requires you to know what you'll plan to do
>> later. 4.5.5 doesn't complain because that version is too old for the
>> GROMACS build system to know the difference between your nodes, so it can
>> do nothing wrong (but also nothing good).
>>
>> Mark
>>
>> On Fri, Oct 16, 2015 at 5:21 PM Ana Marija <sokovic.anamarija at gmail.com>
>> wrote:
>>
>>> HI,
>>>
>>> I installed Gromacs 4.6.7 with plumed 2.2.0, also I generated input files
>>> using this gromacs.
>>> But I am getting this error:
>>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
>>> _pmiu_daemon(SIGCHLD): [NID 00029] [c0-0c0s1n3] [Thu Oct 15 15:25:51
>>> 2015]
>>> PE RANK 0 exit signal Segmentation fault
>>>
>>> But when I use imput files generated with gromacs 4.5.5  with gromacs
>>> 4.6.7
>>> it works.
>>> I don't understand this -- is gromacs-4.6.7 is a flaw version that can
>>> not
>>> generate input files?
>>> And it not what I am doing wrong in my installation?
>>>
>>> I installed 4.6.7  via following process:
>>>
>>> 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 -fPIC
>>> CXX=CC
>>> CXXFLAGS=-O -fPIC
>>> CXXFLAGS_NOOPENMP=-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_EXTERNAL_BLAS=1
>>> -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1
>>> -D__PLUMED_HAS_MPI=1 -D__PLUMED_HAS_CLOCK_GETTIME=1
>>> -D__PLUMED_HAS_GETTIMEOFDAY=1 -D__PLUMED_HAS_READDIR_R=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/new/gromacs/lib2
>>> LIBS=-ldl
>>> SOEXT=
>>> LD=CC
>>> LDSO=CC -shared
>>> GCCDEP=CC
>>> prefix=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0
>>> program_transform_name=s,x,x,
>>> program_can_run_mpi=yes
>>> program_can_run=yes
>>> LD_RO=ld -r -o
>>> exec_prefix=${prefix}
>>> bindir=${exec_prefix}/bin
>>> libdir=${exec_prefix}/lib
>>> includedir=${prefix}/include
>>> datarootdir=${prefix}/share
>>> datadir=${datarootdir}
>>> docdir=${datarootdir}/doc/plumed
>>> htmldir=${docdir}
>>> program_name=plumed
>>> ###
>>>
>>> make
>>> make install
>>>
>>> export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH
>>>
>>> #1. Make a directory for modulefiles (e.g.
>>> /lustre/beagle2/ams/modulefiles/)
>>> #2. Copy file
>>> /lustre/beagle2/ams/groplu/plumed-2.1.1/lib/plumed/src/lib/modulefile
>>> into
>>> /lustre/beagle2/ams/modulefiles/plumed/2.1.1/
>>> #3. type "module use /lustre/beagle2/ams/modulefiles/"
>>> #4. type "module load plumed/2.1.1"
>>>
>>> export PATH=/lustre/beagle2/ams/groplu/plumed-2.1.1/bin:$PATH
>>> module use /lustre/beagle2/ams/modulefiles/
>>> module load plumed/2.1.1
>>>
>>> ### 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/groplu/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/groplu/lib:$CMAKE_LIBRARY_PATH"
>>>
>>> #in /lustre/beagle2/ams/groplu make directory lib
>>>
>>> ams at login1:/lustre/beagle2/ams/lib>ln -s
>>> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
>>> ams at login1:/lustre/beagle2/ams/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/lib64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/default/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/default/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/groplu/gromacs-4.6.7/build
>>> -DGMX_X11=OFF -DGMX_BLAS_USER=/lustre/beagle2/ams/groplu/lib/libblas.a
>>> -DGMX_LAPACK_USER=/lustre/beagle2/ams/groplu/lib/liblapack.a
>>> -DCMAKE_SKIP_RPATH=ON
>>>
>>>
>>> make
>>> make install
>>>
>>> Any help with this would be greatly appreciated,
>>>
>>> Thanks
>>> Ana
>>> --
>>> 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-request at gromacs.org.
>>>
>>
>