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
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:
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.
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Ansgar Esztermann
DV-Systemadministration
Max-Planck-Institut für biophysikalische Chemie, Abteilung 105
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gmx-users mailing list
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:
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 that processes
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
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
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
[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
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
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
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 ... and
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