[gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Ana Marija sokovic.anamarija at gmail.com
Fri Oct 23 21:06:41 CEST 2015 

is there is anywhere installation instruction page for gromacs 5.1? like
there is for gromacs 5.0

and did any of the basic flags for cmake changed?

On Fri, Oct 23, 2015 at 1:44 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> On Fri, Oct 23, 2015 at 7:52 PM Ana Marija <sokovic.anamarija at gmail.com>
> wrote:
>
>> after cmake step I got this:
>> CMake Warning:
>>   Manually-specified variables were not used by the project:
>>
>>     BUILD_SHARED_EXE
>>
>
> This doesn't exist, don't use it.
>
>
>>     GMX_BUILD_SHARED_EXE
>>
>
> This doesn't exist in 5.0.4, because we added it after then. That's
> awkward because PLUMED only claims to support 5.0.4. Probably later 5.0.x
> are fine if one was to make a frankenstein, but since PLUMED 2.2 supports
> 5.1, use that.
>
>
>>     GMX_FORCE_CXX
>>
>
> This was only present in GROMACS 4.6, as it is no longer useful in 5.x.
>
>
>>     MPI_LIBRARY
>>
>
> This is not useful at all - that's what cray's MPI wrapper compilers are
> for.
>
> Mark
>
>
>> my cmake was 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
>> -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/4.9.2/snos/lib64/libgfortran.a;/opt/gcc/4.9.2/snos/lib64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/default/lib64/libalpsutil.a;/opt/gcc/4.9.2/snos/lib64/libgomp.a;/opt/gcc/4.9.2/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/new/gromacs/gromacs-5.0.4/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 -DBUILD_SHARED_EXE=OFF -DGMX_BUILD_SHARED_EXE=OFF
>>
>> can you please let me know what I am doing wrong?
>>
>> On Fri, Oct 23, 2015 at 12:06 PM, Mark Abraham <mark.j.abraham at gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> I don't know what's going to work. Every machine is precious individual
>>> snowflake. Try it :-)
>>>
>>> Mark
>>>
>>> On Fri, Oct 23, 2015 at 7:04 PM Ana Marija <sokovic.anamarija at gmail.com>
>>> wrote:
>>>
>>>> thanks, I do I need to set?
>>>>
>>>> export CFLAGS="-static"
>>>> export CXXFLAGS="-static"
>>>>
>>>> before cmake step?
>>>>
>>>> On Fri, Oct 23, 2015 at 12:03 PM, Mark Abraham <
>>>> mark.j.abraham at gmail.com> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I think -DGMX_BUILD_SHARED_EXE=off is supposed to handle this - see
>>>>> http://www.gromacs.org/Documentation/Installation_Instructions_5.0#static-linking.
>>>>> Or there are environment variables you can set that force the Cray tools to
>>>>> do dynamic vs static linking - check your local docs.
>>>>>
>>>>> As you can see on that Redmine, we're trying to get Cray to be useful
>>>>> solving these problems in a general way, but progress is slow :-(
>>>>>
>>>>> Mark
>>>>>
>>>>> On Fri, Oct 23, 2015 at 6:17 PM Ana Marija <
>>>>> sokovic.anamarija at gmail.com> wrote:
>>>>>
>>>>>> or should I do just this before cmake step?
>>>>>>
>>>>>> export CFLAGS="-static"
>>>>>> export CXXFLAGS="-static"
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Fri, Oct 23, 2015 at 11:12 AM, Ana Marija <
>>>>>> sokovic.anamarija at gmail.com> wrote:
>>>>>>
>>>>>>> the above was reported here as a bug, but I am not sure where and
>>>>>>> how should I put this flag: CFLAGS=CXXFLAGS=-static
>>>>>>>
>>>>>>> http://redmine.gromacs.org/issues/1641
>>>>>>>
>>>>>>> does is just go under cmake like: -DCFLAGS=CXXFLAGS=-static or?
>>>>>>>
>>>>>>> On Fri, Oct 23, 2015 at 10:51 AM, Ana Marija <
>>>>>>> sokovic.anamarija at gmail.com> wrote:
>>>>>>>
>>>>>>>> HI Everybody,
>>>>>>>>
>>>>>>>> I got cmake/3.3.2 installed so I decided to install gromacs 5.0.4
>>>>>>>> with plumed 2.2.0
>>>>>>>>
>>>>>>>> but I got this error during "make" step of gromacs:
>>>>>>>>
>>>>>>>> 100%] Linking CXX executable ../../bin/gmx_mpi
>>>>>>>> /usr/lib/../lib64/librt.a(clock_gettime.o): In function
>>>>>>>> `hp_timing_gettime':
>>>>>>>> /usr/src/packages/BUILD/glibc-2.11.3/rt/../sysdeps/unix/clock_gettime.c:65:
>>>>>>>> undefined reference to `_dl_cpuclock_offset'
>>>>>>>> collect2: error: ld returned 1 exit status
>>>>>>>> make[2]: *** [bin/gmx_mpi] Error 1
>>>>>>>> make[1]: *** [src/programs/CMakeFiles/gmx.dir/all] Error 2
>>>>>>>>
>>>>>>>> my recipe is bellow and I am doing this on Cray XE6 machine, please
>>>>>>>> let me know what I can be doing wrong:
>>>>>>>>
>>>>>>>> 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
>>>>>>>>
>>>>>>>> #download it from here: http://www.plumed-code.org/get-it
>>>>>>>> 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:$PATH
>>>>>>>>
>>>>>>>> #1. Make a directory for modulefiles (e.g.
>>>>>>>> /lustre/beagle2/ams/new/modulefiles/)
>>>>>>>> #2. Copy file: cp
>>>>>>>> /lustre/beagle2/ams/new/gromacs/plumed-2.2.0/lib/plumed/modulefile
>>>>>>>> /lustre/beagle2/ams/new/modulefiles/plumed/2.2.0/
>>>>>>>> #3. type "module use /lustre/beagle2/ams/new/modulefiles/"
>>>>>>>> #4. type "module load plumed/2.2.0"
>>>>>>>>
>>>>>>>> export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH
>>>>>>>> module use /lustre/beagle2/ams/new/modulefiles/
>>>>>>>> module load plumed/2.2.0
>>>>>>>>
>>>>>>>> ### instal gromacs-5.0.4
>>>>>>>> wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.4.tar.gz
>>>>>>>> tar zxvf gromacs-5.0.4.tar.gz
>>>>>>>> cd gromacs-5.0.4/
>>>>>>>> ams at login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.0.4>plumed-patch
>>>>>>>> -p --static
>>>>>>>>
>>>>>>>>
>>>>>>>> PLUMED patching tool
>>>>>>>>
>>>>>>>> 1) amber14        4) gromacs-5.0.4    7) namd-2.8
>>>>>>>> 2) gromacs-4.5.7    5) gromacs-5.1.0    8) namd-2.9
>>>>>>>> 3) gromacs-4.6.7    6) lammps-6Apr13    9) qespresso-5.0.2
>>>>>>>>
>>>>>>>> Choose the best matching code/version:4
>>>>>>>>
>>>>>>>> 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
>>>>>>>>
>>>>>>>> cd /lustre/beagle2/ams/new/gromacs/gromacs-5.0.4/build
>>>>>>>>
>>>>>>>> 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/4.9.2/snos/lib64/libgfortran.a;/opt/gcc/4.9.2/snos/lib64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/default/lib64/libalpsutil.a;/opt/gcc/4.9.2/snos/lib64/libgomp.a;/opt/gcc/4.9.2/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/new/gromacs/gromacs-5.0.4/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
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Thu, Oct 22, 2015 at 12:27 PM, Ana Marija <
>>>>>>>> sokovic.anamarija at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Thanks everybody for all your help!
>>>>>>>>>
>>>>>>>>> On Thu, Oct 22, 2015 at 12:20 PM, Mark Abraham <
>>>>>>>>> mark.j.abraham at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> On Thu, Oct 22, 2015 at 6:58 PM Ana Marija <
>>>>>>>>>> sokovic.anamarija at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> I just tried to install it with:
>>>>>>>>>>> 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_GPU=OFF -DGMX_MPI=OFF
>>>>>>>>>>> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
>>>>>>>>>>> -DGMX_X11=OFF
>>>>>>>>>>>
>>>>>>>>>>> but the error is the same as above.
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> It can't be if you've done it properly. Use a new, empty build
>>>>>>>>>> directory.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> My goal with this installation (without cross compiler) was to
>>>>>>>>>>> use it to generate input files and than use another installation of gromacs
>>>>>>>>>>> compiled with cross compilers to complete the run. Where I would use the
>>>>>>>>>>> same version of gromacs  in both cases, 4.6.7. Can you please confirm me
>>>>>>>>>>> that this is acceptable approach?
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Yes, but needlessly complex. You can run grompp anywhere, copy
>>>>>>>>>> the file to the Cray, and use the resulting .tpr on the compute nodes, like
>>>>>>>>>> I said a while ago.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> The reason why I can't use newer version of gromacs is that I
>>>>>>>>>>> only have cmake 2.8.4 on this machine and it is impossible to install newer
>>>>>>>>>>> version of cmake because it is tied to gnu version we got from Cray etc.
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Perhaps Cray supplied a cmake, but it doesn't run on the compute
>>>>>>>>>> nodes, and has nothing at all to do with the back end compilers, and your
>>>>>>>>>> system admins can and should be willing to download and install a more
>>>>>>>>>> recent cmake for you and everybody else :-)
>>>>>>>>>>
>>>>>>>>>> Mark
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> On Thu, Oct 22, 2015 at 11:51 AM, Szilárd Páll <
>>>>>>>>>>> sin.pecado at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> On Thu, Oct 22, 2015 at 6:34 PM, Ana Marija <
>>>>>>>>>>>> sokovic.anamarija at gmail.com> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> I installed it via:
>>>>>>>>>>>>> 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 -DCMAKE_SKIP_RPATH=ON
>>>>>>>>>>>>>
>>>>>>>>>>>>> then I was running it on login nodes via:
>>>>>>>>>>>>>
>>>>>>>>>>>>> /lustre/beagle2/ams/gro/gromacs-4.6.7/build/bin/grompp -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
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> but I didn't get .tpr file, and output was this:
>>>>>>>>>>>>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
>>>>>>>>>>>>> Generated 1081 of the 1081 non-bonded parameter combinations
>>>>>>>>>>>>> Generating 1-4 interactions: fudge = 0.5
>>>>>>>>>>>>> Generated 994 of the 1081 1-4 parameter combinations
>>>>>>>>>>>>>
>>>>>>>>>>>>> -------------------------------------------------------
>>>>>>>>>>>>> Program grompp, VERSION 4.6.7
>>>>>>>>>>>>> Source code file:
>>>>>>>>>>>>> /lustre/beagle2/ams/gro/gromacs-4.6.7/src/kernel/toppush.c, line: 1803
>>>>>>>>>>>>>
>>>>>>>>>>>>> Fatal error:
>>>>>>>>>>>>> [ file tip3p.itp, line 39 ]:
>>>>>>>>>>>>> Atom index (1) in settles out of bounds (1-0).
>>>>>>>>>>>>> This probably means that you have inserted topology section
>>>>>>>>>>>>> "settles"
>>>>>>>>>>>>> in a part belonging to a different molecule than you intended
>>>>>>>>>>>>> to.
>>>>>>>>>>>>> In that case move the "settles" section to the right molecule.
>>>>>>>>>>>>>
>>>>>>>>>>>>> can you please advise what should I do in this situation?
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> As Justin said, this isn't an issue with the GROMACS build
>>>>>>>>>>>> anymore (but rather with the inputs). So it seems that the original problem
>>>>>>>>>>>> is solved - unless you really need to run grompp on the compute nodes.
>>>>>>>>>>>>
>>>>>>>>>>>> BTW, I hope you know that 4.6.7 is a rather old and outdated
>>>>>>>>>>>> version; the 5.0 and 5.1 series has been released since and the former is
>>>>>>>>>>>> AFAIK supported by PLUMED!
>>>>>>>>>>>>
>>>>>>>>>>>> Cheers,
>>>>>>>>>>>> --
>>>>>>>>>>>> Szilárd
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Thu, Oct 22, 2015 at 11:06 AM, Ana Marija <
>>>>>>>>>>>>> sokovic.anamarija at gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> so is it ok to try 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 -DCMAKE_SKIP_RPATH=ON
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Thu, Oct 22, 2015 at 11:03 AM, Mark Abraham <
>>>>>>>>>>>>>> mark.j.abraham at gmail.com> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Your blas and lapack were compiled with gfortran, but in a
>>>>>>>>>>>>>>> way that they require that one links further dependencies to use them later
>>>>>>>>>>>>>>> on. So compile them better, or use dynamic linking.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> But 99.9% of GROMACS users do not need to get involved with
>>>>>>>>>>>>>>> this, so just leave GMX_BLAS_USER and GMX_BLAS_LAPACK unset and GROMACS
>>>>>>>>>>>>>>> will use its internal versions.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Mark
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>
>>

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