[gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Ana Marija sokovic.anamarija at gmail.com
Thu Oct 22 17:53:51 CEST 2015 

after make step I am getting this errors gfortran related:

cunmqr.f:(.text+0x755): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(zunmrq.o): In function
`__sci_zunmrq_':
zunmrq.f:(.text+0x63e): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(zunmrq.o):zunmrq.f:(.text+0x6f6):
more undefined references to `_gfortran_concat_string' follow
/lustre/beagle2/ams/gro/lib/libblas.a(irt_po_complex_serial.o): In function
`irt_po_complex_serial_':
irt_po_complex_serial.f90:(.text+0x1294): undefined reference to
`_gfortran_os_error'
irt_po_complex_serial.f90:(.text+0x12a2): undefined reference to
`_gfortran_runtime_error'
/lustre/beagle2/ams/gro/lib/libblas.a(dormtr.o): In function
`__sci_dormtr_':
dormtr.f:(.text+0x322): undefined reference to `_gfortran_concat_string'
dormtr.f:(.text+0x4ea): undefined reference to `_gfortran_concat_string'
dormtr.f:(.text+0x549): undefined reference to `_gfortran_concat_string'
dormtr.f:(.text+0x589): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(sormqr.o): In function
`__sci_sormqr_':
sormqr.f:(.text+0x2e5): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(sormqr.o):sormqr.f:(.text+0x755):
more undefined references to `_gfortran_concat_string' follow
/lustre/beagle2/ams/gro/lib/libblas.a(irt_lu_complex_serial.o): In function
`irt_lu_complex_serial_':
irt_lu_complex_serial.f90:(.text+0x1299): undefined reference to
`_gfortran_os_error'
irt_lu_complex_serial.f90:(.text+0x12a7): undefined reference to
`_gfortran_runtime_error'
/lustre/beagle2/ams/gro/lib/libblas.a(shseqr.o): In function
`__sci_shseqr_':
shseqr.f:(.text+0x41a): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(cgesvd.o): In function
`__sci_cgesvd_':
cgesvd.f:(.text+0x3fc): undefined reference to `_gfortran_concat_string'
cgesvd.f:(.text+0x5fb): undefined reference to `_gfortran_concat_string'
cgesvd.f:(.text+0x730): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(dormqr.o): In function
`__sci_dormqr_':
dormqr.f:(.text+0x2e5): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(dormqr.o):dormqr.f:(.text+0x73d):
more undefined references to `_gfortran_concat_string' follow
/lustre/beagle2/ams/gro/lib/libblas.a(zunmql.o): In function
`__sci_zunmql_':
zunmql.f:(.text+0x43): undefined reference to
`_gfortran_get_environment_variable_i4'
zunmql.f:(.text+0x5c): undefined reference to `_gfortran_compare_string'
zunmql.f:(.text+0xbd): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(sormbr.o): In function
`__sci_sormbr_':
sormbr.f:(.text+0x3bf): undefined reference to `_gfortran_concat_string'
sormbr.f:(.text+0x58a): undefined reference to `_gfortran_concat_string'
sormbr.f:(.text+0x5e9): undefined reference to `_gfortran_concat_string'
sormbr.f:(.text+0x629): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(zunmqr.o): In function
`__sci_zunmqr_':
zunmqr.f:(.text+0x43): undefined reference to
`_gfortran_get_environment_variable_i4'
zunmqr.f:(.text+0x5c): undefined reference to `_gfortran_compare_string'
zunmqr.f:(.text+0xbd): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(zgesvd3m.o): In function `zgesvd3m_':
zgesvd3m.f:(.text+0x35b): undefined reference to `_gfortran_concat_string'
zgesvd3m.f:(.text+0x4ef): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(irt_po_real_serial.o): In function
`irt_po_real_serial_':
irt_po_real_serial.f90:(.text+0x10e8): undefined reference to
`_gfortran_os_error'
/lustre/beagle2/ams/gro/lib/libblas.a(zunmrz.o): In function
`__sci_zunmrz_':
zunmrz.f:(.text+0x373): undefined reference to `_gfortran_concat_string'
zunmrz.f:(.text+0x744): undefined reference to `_gfortran_concat_string'
zunmrz.f:(.text+0x7f6): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(cunmbr.o): In function
`__sci_cunmbr_':
cunmbr.f:(.text+0x3ab): undefined reference to `_gfortran_concat_string'
cunmbr.f:(.text+0x57e): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(cunmbr.o):cunmbr.f:(.text+0x5d9):
more undefined references to `_gfortran_concat_string' follow
/lustre/beagle2/ams/gro/lib/libblas.a(irt_lu_real_serial.o): In function
`irt_lu_real_serial_':
irt_lu_real_serial.f90:(.text+0x107f): undefined reference to
`_gfortran_os_error'
/lustre/beagle2/ams/gro/lib/libblas.a(zunmqlint.o): In function
`zunmqlint_':
zunmqlint.f:(.text+0x63c): undefined reference to `_gfortran_concat_string'
zunmqlint.f:(.text+0x755): undefined reference to `_gfortran_concat_string'
/lustre/beagle2/ams/gro/lib/libblas.a(zunmqr_cray_internal.o): In function
`zunmqr_cray_internal_':
zunmqr_cray_internal.f:(.text+0x717): undefined reference to
`_gfortran_concat_string'



I did do this:
cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
-DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
-DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF
-DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=OFF
-DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
-DGMX_X11=OFF -DGMX_BLAS_USER=/lustre/beagle2/ams/gro/lib/libblas.a
-DGMX_LAPACK_USER=/lustre/beagle2/ams/gro/lib/liblapack.a
-DCMAKE_SKIP_RPATH=ON

do I need to specify flag for gfortran and how to do that?


On Thu, Oct 22, 2015 at 10:23 AM, Ana Marija <sokovic.anamarija at gmail.com>
wrote:

> 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
>>>>> >
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