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 <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 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.
