Re: [gmx-users] Gromacs installation problem

2013-07-12 Thread Douglas Houston
Thanks a lot Mark, that worked (after I did "setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/usr/people/douglas/programs/gromacs-4.6.3/install/lib"). Quoting Mark Abraham on Fri, 12 Jul 2013 13:22:01 +0100: On Fri, Jul 12, 2013 at 11:18 AM, Douglas Houston wrote: Hi, I am having trouble in

Re: [gmx-users] Gromacs installation problem

2013-07-12 Thread Mark Abraham
On Fri, Jul 12, 2013 at 11:18 AM, Douglas Houston wrote: > Hi, > > I am having trouble installing Gromacs 4.6.3. > > In bash I am using the following sequence of commands: > > cd gromacs-4.6.3 > mkdir build > cd build > CC=/usr/people/douglas/programs/gcc-4.7.3/installation/bin/gcc > ~/programs/cm

Re: [gmx-users] GROMACS Installation problem: libfftw3f.so.3: cannot open shared object file

2012-05-28 Thread Mark Abraham
On 29/05/2012 3:09 PM, a a wrote: Dear Sir/Madam, Follow the steps below, I have installed fftw library and gromacs as a root. (1) tar -xzvf fftw-3.0.1.tar.gz (2) cd fftw-3.0.1 (3) ./configure --enable-float --enable-threads --enable-shared Here you enabled threads for fftw, which is not re

Re: [gmx-users] Gromacs installation problem @ RHEL5.5 server

2010-10-14 Thread Sikandar Mashayak
hey thanks Sander for bringing my attention to -nt option.. ;) -- sikandar On Thu, Oct 14, 2010 at 6:08 AM, Sander Pronk wrote: > > On 14 Oct 2010, at 05:49 , Sikandar Mashayak wrote: > > > Recently I installed gromacs4.5.1 without mpi support on my workstation > with 8 cores using cmake and m

Re: [gmx-users] Gromacs installation problem @ RHEL5.5 server

2010-10-14 Thread Sander Pronk
On 14 Oct 2010, at 05:49 , Sikandar Mashayak wrote: > Recently I installed gromacs4.5.1 without mpi support on my workstation with > 8 cores using cmake and make -j 8, make install commands ( as suggested on > installation instructions). > > Now when I do mdrun it automatically utilizes all t

Re: [gmx-users] Gromacs installation problem @ RHEL5.5 server

2010-10-13 Thread Sathish
oh ok ok. Then i was started to run demo last 3 hrs back but still its running. How long will take time to complete because its running under one cpu. Any other possible way is there to increase speed. ? On Thu, Oct 14, 2010 at 12:35 PM, Mark Abraham wrote: > On 14/10/2010 1:35 PM, Sathish wrote

Re: [gmx-users] Gromacs installation problem @ RHEL5.5 server

2010-10-13 Thread Sikandar Mashayak
Recently I installed gromacs4.5.1 without mpi support on my workstation with 8 cores using cmake and make -j 8, make install commands ( as suggested on installation instructions). Now when I do mdrun it automatically utilizes all the cores and runs much faster than earlier version (4.0.7) , which

Re: [gmx-users] Gromacs installation problem @ RHEL5.5 server

2010-10-13 Thread Mark Abraham
On 14/10/2010 1:35 PM, Sathish wrote: Thanks for clarifying my doubts. I have started to run demo its working. I have checked processor speed its says only one cpu is running for that program (pdb2gmx). my server configuration (RHEL 5.5) is 2 processor with 6 core, totally 24 processor. I

Re: [gmx-users] Gromacs installation problem @ RHEL5.5 server

2010-10-13 Thread Sathish
Thanks for clarifying my doubts. I have started to run demo its working. I have checked processor speed its says only one cpu is running for that program (pdb2gmx). my server configuration (RHEL 5.5) is 2 processor with 6 core, totally 24 processor. I have set "export NCPU=24" while installing gr

Re: [gmx-users] Gromacs installation problem @ RHEL5.5 server

2010-10-13 Thread Justin A. Lemkul
Sathish wrote: Dear Mark, wow its working. Thank you lot.. As per installation instruction gromacs installed successfully and demo also working. Then i have downloaded test set "gmxtest-4.0.4.tgz". While running i got error message like this, [r...@xxx gmxtest]# ./gmxtest.pl

Re: [gmx-users] Gromacs installation problem @ RHEL5.5 server

2010-10-13 Thread Sathish
Dear Mark, wow its working. Thank you lot.. As per installation instruction gromacs installed successfully and demo also working. Then i have downloaded test set "gmxtest-4.0.4.tgz". While running i got error message like this, [r...@xxx gmxtest]# ./gmxtest.pl all FAILED. Check files in angles1

Re: [gmx-users] Gromacs installation problem @ RHEL5.5 server

2010-10-13 Thread David van der Spoel
On 2010-10-13 10.54, Sathish wrote: Dear Mark, I have one more doubt. How to run "luck". If i run luck anywhere its says command not found.. my installed and binary directory cant find luck program. how to do? without checking luck shall i start to run demo? Instructions are outdat

Re: [gmx-users] Gromacs installation problem @ RHEL5.5 server

2010-10-13 Thread Sathish
Dear Mark, I have one more doubt. How to run "luck". If i run luck anywhere its says command not found.. my installed and binary directory cant find luck program. how to do? without checking luck shall i start to run demo? On Wed, Oct 13, 2010 at 3:19 PM, Mark Abraham wrote: > On 1

Re: [gmx-users] Gromacs installation problem @ RHEL5.5 server

2010-10-12 Thread Mark Abraham
On 13/10/2010 5:01 PM, Mark Abraham wrote: On 13/10/2010 4:55 PM, Sathish wrote: Dear Mark, Thanks for your reply. In my server gromacs installed at "local/gromacs". I have checked out point 8 as you mentioned. It was working with this "source /local/gromacs/bin/GMXRC" command. That's

Re: [gmx-users] Gromacs installation problem @ RHEL5.5 server

2010-10-12 Thread Mark Abraham
On 13/10/2010 4:55 PM, Sathish wrote: Dear Mark, Thanks for your reply. In my server gromacs installed at "local/gromacs". I have checked out point 8 as you mentioned. It was working with this "source /local/gromacs/bin/GMXRC" command. That's all you need to do, in every shell from whi

Re: [gmx-users] Gromacs installation problem @ RHEL5.5 server

2010-10-12 Thread Sathish
Dear Mark, Thanks for your reply. In my server gromacs installed at "local/gromacs". I have checked out point 8 as you mentioned. It was working with this "source /local/gromacs/bin/GMXRC" command. and also tried , entered "local/gromacs/bin" path and calling to GMXRC but it shows error [r.

Re: [gmx-users] Gromacs installation problem @ RHEL5.5 server

2010-10-12 Thread Mark Abraham
- Original Message - From: Sathish Date: Wednesday, October 13, 2010 14:31 Subject: [gmx-users] Gromacs installation problem @ RHEL5.5 server To: gmx-users@gromacs.org > Dear all, > I have compiled and installed gromacs 4.5.1 on RHEL5.5 server. I have also > installed openmpi-1.2.8, ff

Re: [gmx-users] gromacs installation problem in ibm powerpc system

2010-05-30 Thread Mark Abraham
- Original Message - From: Sanku M Date: Monday, May 31, 2010 13:00 Subject: [gmx-users] gromacs installation problem in ibm powerpc system To: gmx-users@gromacs.org > Hi,>   I am having a problem in a cluster which is IBM  PowerPC 970MPs and > running SUSE linux and it has IBM XL  C &