[gmx-users] gromacs 4.6.7 plumed -Segmentation fault
Ana Marija
sokovic.anamarija at gmail.com
Fri Oct 23 17:51:27 CEST 2015
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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