[gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[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 at 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 <sin.pecado at gmail.com> wrote:

> On Thu, Oct 22, 2015 at 6:34 PM, Ana Marija <sokovic.anamarija at gmail.com>
> wrote:
>
>> I installed it via:
>> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
>> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
>> -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF
>> -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=OFF
>> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
>> -DGMX_X11=OFF -DCMAKE_SKIP_RPATH=ON
>>
>> then I was running it on login nodes via:
>>
>> /lustre/beagle2/ams/gro/gromacs-4.6.7/build/bin/grompp -f
>> /lustre/beagle2/ruisun/MYCO/Set-1/input/grompp.mdp -c
>> /lustre/beagle2/ruisun/MYCO/Set-1/input/initial.gro -p
>> /lustre/beagle2/ruisun/MYCO/Set-1/input/topol.top -n
>> /lustre/beagle2/ruisun/MYCO/Set-1/input/index.ndx -o ttmeta1.tpr
>>
>>
>> but I didn't get .tpr file, and output was this:
>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
>> Generated 1081 of the 1081 non-bonded parameter combinations
>> Generating 1-4 interactions: fudge = 0.5
>> Generated 994 of the 1081 1-4 parameter combinations
>>
>> -------------------------------------------------------
>> Program grompp, VERSION 4.6.7
>> Source code file:
>> /lustre/beagle2/ams/gro/gromacs-4.6.7/src/kernel/toppush.c, line: 1803
>>
>> Fatal error:
>> [ file tip3p.itp, line 39 ]:
>> Atom index (1) in settles out of bounds (1-0).
>> This probably means that you have inserted topology section "settles"
>> in a part belonging to a different molecule than you intended to.
>> In that case move the "settles" section to the right molecule.
>>
>> can you please advise what should I do in this situation?
>>
>
> As Justin said, this isn't an issue with the GROMACS build anymore (but
> rather with the inputs). So it seems that the original problem is solved -
> unless you really need to run grompp on the compute nodes.
>
> BTW, I hope you know that 4.6.7 is a rather old and outdated version; the
> 5.0 and 5.1 series has been released since and the former is AFAIK
> supported by PLUMED!
>
> Cheers,
> --
> Szilárd
>
>
>
>>
>> On Thu, Oct 22, 2015 at 11:06 AM, Ana Marija <sokovic.anamarija at gmail.com
>> > wrote:
>>
>>> so is it ok to try this?
>>> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
>>> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
>>> -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF
>>> -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=OFF
>>> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
>>> -DGMX_X11=OFF -DCMAKE_SKIP_RPATH=ON
>>>
>>>
>>>
>>> On Thu, Oct 22, 2015 at 11:03 AM, Mark Abraham <mark.j.abraham at gmail.com
>>> > wrote:
>>>
>>>> Hi,
>>>>
>>>> Your blas and lapack were compiled with gfortran, but in a way that
>>>> they require that one links further dependencies to use them later on. So
>>>> compile them better, or use dynamic linking.
>>>>
>>>> But 99.9% of GROMACS users do not need to get involved with this, so
>>>> just leave GMX_BLAS_USER and GMX_BLAS_LAPACK unset and GROMACS will use its
>>>> internal versions.
>>>>
>>>> Mark
>>>>
>>>>
>>>
>>
>