Re: [gmx-users] Gromacs 3.3.3 on Lion Xgrid

On Mar 6, 2012, at 22:03 , Benjamin Hall wrote: > Hi > > I realise this is a question regarding an old version of gromacs on a new OS, > but I was hoping that someone could tell me why grompp might fail in 3.3.3 > with the following error > > llvm-gcc-4.2: error trying to exec 'i686-apple-dar

Re: [gmx-users] parallel running

On Mar 8, 2011, at 12:00 , mohsen ramezanpour wrote: > >> > Besides when I used the following command I get an executeable Error: >> > mpirun -np 8 mdrun_mpi -deffnm output & >> >> What is the error message? > > the Error is: > Failed to find the following executable: > > Host:

Re: [gmx-users] parallel running

>> You don't use qsub or bsub? > > No,What is these?How can I prepare and use them? They are commands to submit jobs to batch systems. A. -- Ansgar Esztermann DV-Systemadministration Max-Planck-Institut für biophysikalische Chemie, Abteilung 105 -- gmx-users mailing listgmx-users@gromac

Re: [gmx-users] parallel running

On Mar 8, 2011, at 10:26 , mohsen ramezanpour wrote: > 4- nohup mpirun -np 8 mdrun -deffnm output & > > The result is running mdrun on one node(compute-0-1) (on its 4 CPUs) That's just as it is supposed to be. > Besides when I used the following command I get an executeable Error: >

Re: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

>>> Thanks for the information; the OpenMPI recommendation is probably because >>> OpenMPI goes to great lengths trying to avoid process migration. The >>> numactl doesn't prevent migration as far as I can tell: it controls where >>> memory gets allocated if it's NUMA. >> My understanding is t

Re: [gmx-users] Gromacs build error

Hi, > What does this switch do? When I do set the variable, it cannot even create > the Makefiles: According to the manpage, it enables the __m128 types. The original error message points to a line containing such a type. I've looked at the PGI 10.3 manpage -- other versions may behave differe

Re: [gmx-users] Gromacs build error

Hi, > I am trying to build Gromacs 4.5 from source using the Portland Group > compiler: Have you tried adding -Mm128 to CFLAGS? A. -- Ansgar Esztermann DV-Systemadministration Max-Planck-Institut für biophysikalische Chemie, Abteilung 105 -- gmx-users mailing listgmx-users@gromacs.org h

[gmx-users] Backing up trajectories

Hi everyone, I am just wondering how backups of Gromacs trajectories are handled "out there". We are using TSM. The system is very reliable, but it does not scale well in conjunction with Gromacs: trajectories can get very large when -append is used (dozens of Gigabytes), but TSM cannot do blo

Re: [gmx-users] installation: gromacs on Mac.10.5.8 leopard

[This should have gone to the list] Dear Ali, gcc should be in /usr/bin (or some other bin, if you do not use Apple's compiler), not in /usr/lib nor /usr/local/lib. Do you have the developer tools installed? If not, get them from http://developer.apple.com/mac/ (they should also be on the OS D

Re: [gmx-users] installation: gromacs on Mac.10.5.8 leopard

On Jul 21, 2010, at 11:07 , KACHMAR Ali wrote: > checking whether the MPI cc command works... configure: error: Cannot compile > and link MPI code with mpicc This is the immediate problem: something goes wrong when compiling a test program with mpicc. If you look into the configure log, you s

Re: [gmx-users] question about installing gromacs on a mac

On May 5, 2010, at 18:15 , Emily Curtis wrote: > > checking for mkl.h... yes > checking for DftiComputeForward in -lmkl... no > configure: error: Cannot find Intel Math Kernel Library >= 6.0 > > > I don't understand why it is not finding my Math Kernal Library. I also do > not understand what

Re: [gmx-users] Reg: Running gromacs on a condor cluster

On Apr 30, 2010, at 14:46 , Rohit Farmer wrote: > > Hi everyone.. > > I just made a small two node condor cluster and was trying to run gromacs on > it ... so i used the vanilla environment and placed the gromacs mdrun command > in a shell script and used the shell script to run the command ...