subject:"Re\: \[gmx\-users\] gromacs 4.6.7 plumed \-Segmentation fault"

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-23 Thread Mark Abraham

Hi,

On Fri, Oct 23, 2015 at 7:52 PM Ana Marija 
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 
> 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 
>> 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 >> > 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 
 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.anamar...@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.anamar...@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@login1:/lustre/beagle2/ams/lib2>ln -s
>>>

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-23 Thread Ana Marija

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 
wrote:

> Hi,
>
> On Fri, Oct 23, 2015 at 7:52 PM Ana Marija 
> 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 
>> 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 
>>> 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.abra...@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.anamar...@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.anamar...@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.anamar...@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

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-23 Thread Ana Marija

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 
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@login1:/lustre/beagle2/ams/lib2>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
> ams@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
>
> ###Makefile.conf should look like this, if not please delete all
> extra stuff before proceeding to make step
> 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@login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.0.4>plumed-patch -p
> --static
>
>
> PLUMED patching tool
>
> 1) amber144) gromacs-5.0.47) namd-2.8
> 2) gromacs-4.5.75) gromacs-5.1.08) namd-2.9
> 3) gromacs-4.6.76) lammps-6Apr139) 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@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@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
>

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-23 Thread Ana Marija

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@login1:/lustre/beagle2/ams/lib2>ln -s
/opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
ams@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

###Makefile.conf should look like this, if not please delete all
extra stuff before proceeding to make step
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@login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.0.4>plumed-patch -p
--static


PLUMED patching tool

1) amber144) gromacs-5.0.47) namd-2.8
2) gromacs-4.5.75) gromacs-5.1.08) namd-2.9
3) gromacs-4.6.76) lammps-6Apr139) 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@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@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

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-23 Thread Ana Marija

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 
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 
> 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@login1:/lustre/beagle2/ams/lib2>ln -s
>> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
>> ams@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
>>
>> ###Makefile.conf should look like this, if not please delete all
>> extra stuff before proceeding to make step
>> 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@login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.0.4>plumed-patch -p
>> --static
>>
>>
>> PLUMED patching tool
>>
>> 1) amber144) gromacs-5.0.47) namd-2.8
>> 2) gromacs-4.5.75) gromacs-5.1.08) namd-2.9
>> 3) gromacs-4.6.76) lammps-6Apr139) 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@login1:/lustre/beagle2/ams/new/gromacs/lib>ln -s
>> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
>>

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-23 Thread Mark Abraham

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 
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 
> 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 
>> 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.anamar...@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.anamar...@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@login1:/lustre/beagle2/ams/lib2>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
> ams@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
>
> ###Makefile.conf should look like this, if not please delete
> all extra stuff before proceeding to make step
> 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
>

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-23 Thread Mark Abraham

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 
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 
> 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 > > 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@login1:/lustre/beagle2/ams/lib2>ln -s
>>> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
>>> ams@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
>>>
>>> ###Makefile.conf should look like this, if not please delete all
>>> extra stuff before proceeding to make step
>>> 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@login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.0.4>plumed-patch
>>> -p --static
>>>
>>>
>>> PLUMED patching tool
>>>

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-23 Thread Ana Marija

after cmake step I got this:
CMake Warning:
  Manually-specified variables were not used by the project:

BUILD_SHARED_EXE
GMX_BUILD_SHARED_EXE
GMX_FORCE_CXX
MPI_LIBRARY

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 
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 
> 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 
>> 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 
>>> 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.anamar...@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.anamar...@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@login1:/lustre/beagle2/ams/lib2>ln -s
>> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
>> ams@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
>>
>> ###Makefile.conf should look like this, if not please delete
>> all extra stuff before proceeding to make step
>> CC=cc
>>

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-23 Thread Ana Marija

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 
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 
> 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 > > 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.anamar...@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@login1:/lustre/beagle2/ams/lib2>ln -s
 /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
 ams@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

 ###Makefile.conf should look like this, if not please delete
 all extra stuff before proceeding to make step
 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

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-23 Thread Ana Marija

I tried installing gromacs 5.1 and this is what I got:

ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1/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-5.1/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
-- The C compiler identification is GNU 4.9.2
-- The CXX compiler identification is GNU 4.9.2
-- Check for working C compiler: /opt/cray/craype/2.4.0/bin/cc
-- Check for working C compiler: /opt/cray/craype/2.4.0/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /opt/cray/craype/2.4.0/bin/CC
-- Check for working CXX compiler: /opt/cray/craype/2.4.0/bin/CC -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Error at CMakeLists.txt:61 (message):
  GROMACS cannot be installed into the build tree, choose a different
  location for CMAKE_INSTALL_PREFIX


-- Configuring incomplete, errors occurred!

Can you please advise

On Fri, Oct 23, 2015 at 2:06 PM, Ana Marija 
wrote:

> 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 
> wrote:
>
>> Hi,
>>
>> On Fri, Oct 23, 2015 at 7:52 PM Ana Marija 
>> 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 >> > wrote:
>>>
 Hi,

 I don't know

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-23 Thread Mark Abraham

Hi,

http://manual.gromacs.org/documentation/5.1/index.html


On Fri, Oct 23, 2015 at 9:39 PM Ana Marija 
wrote:

> I tried installing gromacs 5.1 and this is what I got:
>
> ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1/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-5.1/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
> -- The C compiler identification is GNU 4.9.2
> -- The CXX compiler identification is GNU 4.9.2
> -- Check for working C compiler: /opt/cray/craype/2.4.0/bin/cc
> -- Check for working C compiler: /opt/cray/craype/2.4.0/bin/cc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Detecting C compile features
> -- Detecting C compile features - done
> -- Check for working CXX compiler: /opt/cray/craype/2.4.0/bin/CC
> -- Check for working CXX compiler: /opt/cray/craype/2.4.0/bin/CC -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- Detecting CXX compile features
> -- Detecting CXX compile features - done
> CMake Error at CMakeLists.txt:61 (message):
>   GROMACS cannot be installed into the build tree, choose a different
>   location for CMAKE_INSTALL_PREFIX
>
>
> -- Configuring incomplete, errors occurred!
>
> Can you please advise
>

I don't know to be more specific than "choose a different location for
CMAKE_INSTALL_PREFIX." You chose something that won't work.

Mark


>
> On Fri, Oct 23, 2015 at 2:06 PM, Ana Marija 
> wrote:
>
>> 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 
>> wrote:
>>
>>> Hi,
>>>
>>> On Fri, Oct 23, 2015 at 7:52 PM Ana Marija 
>>> 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

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-23 Thread Ana Marija

I am now trying to install gromacs 5.1 on Cray XE6

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"

then in:
ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1>

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/build -DGMX_X11=OFF
-DGMX_EXTERNAL_BLAS=OFF -DGMX_EXTERNAL_LAPACK=OFF

-- Using default library suffix: "_mpi"
-- Found PythonInterp: /usr/bin/python (found version "2.6.9")
CMake Error at cmake/FindSphinx.cmake:52 (string):
  string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
  command.
Call Stack (most recent call first):
  docs/CMakeLists.txt:62 (find_package)


-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_DEPRECATED_REGISTER
-- Performing Test HAS_NO_DEPRECATED_REGISTER - Success
-- Configuring incomplete, errors occurred!


Can you please advise me what to do?
Also do I need to use -DCMAKE_PREFIX_PATH= flag  or any other flag?



On Thu, Oct 22, 2015 at 11:51 AM, Szilárd Páll  wrote:

> On Thu, Oct 22, 2015 at 6:34 PM, Ana Marija 
> 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 > > 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

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-22 Thread Mark Abraham

Hi,

On Thu, Oct 22, 2015 at 6:58 PM Ana Marija 
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 
> wrote:
>
>> On Thu, Oct 22, 2015 at 6:34 PM, Ana Marija 
>> 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.anamar...@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.abra...@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
>
>

>>>
>>
>
-- 
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

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-22 Thread Ana Marija

Thanks everybody for all your help!

On Thu, Oct 22, 2015 at 12:20 PM, Mark Abraham 
wrote:

> Hi,
>
> On Thu, Oct 22, 2015 at 6:58 PM Ana Marija 
> 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 
>> wrote:
>>
>>> On Thu, Oct 22, 2015 at 6:34 PM, Ana Marija >> > 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.anamar...@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.abra...@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

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-22 Thread Barnett, James W

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@login1:/lustre/beagle2/ams/lib2>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
> ams@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
> 
> ###Makefile.conf should look like this, if not please delete all
> extra stuff before proceeding to make step
> 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@login1:/lustre/beagle2/ams/new/gromacs/gromacs-4.6.7>plumed-patch -p
> --static
> 
> 
> PLUMED patching tool
> 
> 1) amber143) gromacs-4.6.75) lammps-6Apr137) namd-2.9
> 2) gromacs-4.5.54) gromacs-5.06) namd-2.88) 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@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@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

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-22 Thread Ana Marija

if I do that that I got: Illegal Instruction error
which makes sense because I compiled gromacs with cross compiler for
compute nodes

On Thu, Oct 22, 2015 at 9:23 AM, Barnett, James W 
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@login1:/lustre/beagle2/ams/lib2>ln -s
> > /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
> > ams@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
> >
> > ###Makefile.conf should look like this, if not please delete all
> > extra stuff before proceeding to make step
> > 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@login1:/lustre/beagle2/ams/new/gromacs/gromacs-4.6.7>plumed-patch -p
> > --static
> >
> >
> > PLUMED patching tool
> >
> > 1) amber143) gromacs-4.6.75) lammps-6Apr137) namd-2.9
> > 2) gromacs-4.5.54) gromacs-5.06) namd-2.88)
> 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@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@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
> >

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-22 Thread Szilárd Páll

On Thu, Oct 22, 2015 at 4:27 PM, Ana Marija 
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 
> 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@login1:/lustre/beagle2/ams/lib2>ln -s
> > > /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
> > > ams@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
> > >
> > > ###Makefile.conf should look like this, if not please delete
> all
> > > extra stuff before proceeding to make step
> > > 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@login1:/lustre/beagle2/ams/new/gromacs/gromacs-4.6.7>plumed-patch
> -p
> > > --static
> > >
> > >
> > > PLUMED patching tool
> > >
> > > 1) amber143) gromacs-4.6.75) lammps-6Apr137) namd-2.9
> > > 2) gromacs-4.5.54) gromacs-5.06) namd-2.88)
> > 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@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@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
> > >
> >
>

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-22 Thread Szilárd Páll

Hi Ana Marija,

This seems to have little or nothing to do with PLUMED. Given the
presentation it is quite unclear to me:
i) what exactly is the issue (grompp segfault?); what happens if you use
unmodified GROMACS source? What if you run on the login node (binaries
compiled for it). Do other tools, e.g. mdrun work?
ii) Where are these build steps from, they look strange (e.g. you shouldn't
have to set MPI_LIBRARY or symlink libsci_gnu).

BTW, you can generate your tpr input locally or anywhere else, you don't
need to do it on the machine where you're planning ot run int.

Cheers,
--
Szilárd

On Wed, Oct 21, 2015 at 5:20 PM, 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@login1:/lustre/beagle2/ams/lib2>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
> ams@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
>
> ###Makefile.conf should look like this, if not please delete all
> extra stuff before proceeding to make step
> 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@login1:/lustre/beagle2/ams/new/gromacs/gromacs-4.6.7>plumed-patch -p
> --static
>
>
> PLUMED patching tool
>
> 1) amber143) gromacs-4.6.75) lammps-6Apr137) namd-2.9
> 2) gromacs-4.5.54) gromacs-5.06) namd-2.88) 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@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@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/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

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-22 Thread Ana Marija

also I tried to install it with difference versions of gcc:
gcc/4.7.2  gcc/4.8.1  gcc/4.9.1  gcc/4.9.2

but segmentation error is still the same

On Wed, Oct 21, 2015 at 10:20 AM, 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@login1:/lustre/beagle2/ams/lib2>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
> ams@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
>
> ###Makefile.conf should look like this, if not please delete all
> extra stuff before proceeding to make step
> 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@login1:/lustre/beagle2/ams/new/gromacs/gromacs-4.6.7>plumed-patch -p
> --static
>
>
> PLUMED patching tool
>
> 1) amber143) gromacs-4.6.75) lammps-6Apr137) namd-2.9
> 2) gromacs-4.5.54) gromacs-5.06) namd-2.88) 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@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@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/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/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

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-22 Thread Ana Marija

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 
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 
> 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 
>> wrote:
>>
>>> On Thu, Oct 22, 2015 at 4:27 PM, Ana Marija >> > 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 
 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@login1:/lustre/beagle2/ams/lib2>ln -s
 > > /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
 > >

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-22 Thread Szilárd Páll

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 
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 
> wrote:
>
>> On Thu, Oct 22, 2015 at 4:27 PM, Ana Marija 
>> 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 
>>> 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@login1:/lustre/beagle2/ams/lib2>ln -s
>>> > > /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
>>> > > ams@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

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-22 Thread Ana Marija

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?

On Thu, Oct 22, 2015 at 11:06 AM, Ana Marija 
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 
> 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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Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-22 Thread Szilárd Páll

On Thu, Oct 22, 2015 at 6:06 PM, Ana Marija 
wrote:

> so is it ok to try this?
>

Trying rarely hurts. :)

> 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
>

The CMKAE_SKIP_RPATH=ON part is only needed if you need/want to build
static binaries for the compute nodes.  As the Cray wrappers do some magic
behind the scenes in order to link statically, this ends up confusig cmake
which assumes that the resulting binaries will be dynamically linked.
Hence, the last step of setting the RPATH would fail (except if you tell
the Cray wrappers to stop the trickery and link dynamically: export
CRAYPE_LINK_TYPE=dynamic').

To build dynamically linked binaries for login nodes omitting RPATH is not
be necessary - and in fact it makes your/the users' life harder because
LD_LIBRARY_PATH will need to be set whenever running tools.

>
>
>
> On Thu, Oct 22, 2015 at 11:03 AM, Mark Abraham 
> 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
> >
> >
> --
> 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-requ...@gromacs.org.
>
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Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-22 Thread Justin Lemkul




On 10/22/15 12:34 PM, Ana Marija 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?



The error message itself tells you the most likely problem.  Your topology has 
some formatting or sequence that is broken, causing misinterpretation or 
misapplication of a [ settles ] directive.


-Justin


On Thu, Oct 22, 2015 at 11:06 AM, Ana Marija 
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 
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






--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-22 Thread Mark Abraham

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
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-22 Thread Ana Marija

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 
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
>
>
-- 
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
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Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-22 Thread Ana Marija

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

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

2015-10-22 Thread Ana Marija

where with "complete run" means I would run it later on compute nodes.

On Thu, Oct 22, 2015 at 11:58 AM, Ana Marija 
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.
>
> 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?
>
> 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.
>
>
>
> On Thu, Oct 22, 2015 at 11:51 AM, Szilárd Páll 
> wrote:
>
>> On Thu, Oct 22, 2015 at 6:34 PM, Ana Marija 
>> 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.anamar...@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.abra...@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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* Please search the archive at 
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Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

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