Dear Sir: I am a new user of Chimera, but immediately attracted by this handy software Chimera. Since my model requires a lot of computation time in energy minimization, could you please how to set up the environment for parallel computation of energy minimization in Chimera? On one website, it was said, MMTK ENERGY THREADS could be reset for parallel computation. After installation of MMTK, I am confused on how to change parameter in MMTK, and recompile Chimera (or change Chimera settings ). Could you please give me more details about how to set MMTK ENERGY THREADS in Chimera? Sincerely thanks for your advice. Lowie -- Without dream, life is incomplete!
Hi Lowie, You don't have to install MMTK yourself. It is bundled with Chimera. Also, as this post says: [Chimera-users] Parallel run it depends on your platform and personal configuration. So, what platform do you use (Windows/Linux/Mac) and if it's Linux, what shell do you use? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 14, 2012, at 6:56 AM, A-A_lowie li wrote:
Dear Sir:
I am a new user of Chimera, but immediately attracted by this handy software Chimera.
Since my model requires a lot of computation time in energy minimization, could you please how to set up the environment for parallel computation of energy minimization in Chimera?
On one website, it was said, MMTK ENERGY THREADS could be reset for parallel computation.
After installation of MMTK, I am confused on how to change parameter in MMTK, and recompile Chimera (or change Chimera settings ).
Could you please give me more details about how to set MMTK ENERGY THREADS in Chimera?
Sincerely thanks for your advice.
Lowie
-- Without dream, life is incomplete! _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Prof. Eric & other team member: First, thanks for your reply and help. As for the platform of my computer, here is the basic information: Ubuntu, Release 12.04 (precise) 64-bit Kernel Linux 3.2.0-24-generic GNOME 3.4.1 Intel® Core™ i7 CPU 860 @ 2.80GHz × 8 Memory:5.8G As for the shell, i usually use bash :) Please let me know how to change the MMTK_ENERGY_THREADS parameter? Sincerely thanks for your help. Lowie On Fri, Jun 15, 2012 at 1:51 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Lowie, You don't have to install MMTK yourself. It is bundled with Chimera. Also, as this post says:
[Chimera-users] Parallel run<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-September/005499.html>
it depends on your platform and personal configuration. So, what platform do you use (Windows/Linux/Mac) and if it's Linux, what shell do you use?
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Jun 14, 2012, at 6:56 AM, A-A_lowie li wrote:
Dear Sir:
I am a new user of Chimera, but immediately attracted by this handy software Chimera.
Since my model requires a lot of computation time in energy minimization, could you please how to set up the environment for parallel computation of energy minimization in Chimera?
On one website, it was said, MMTK ENERGY THREADS could be reset for parallel computation.
After installation of MMTK, I am confused on how to change parameter in MMTK, and recompile Chimera (or change Chimera settings ).
Could you please give me more details about how to set MMTK ENERGY THREADS in Chimera?
Sincerely thanks for your advice.
Lowie
-- Without dream, life is incomplete! _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Without dream, life is incomplete!
Hi Lowie, On Linux using bash, type this in your shell window before starting Chimera (from that same shell window) to use 2 CPUs (obviously, use a higher number if you want to use more CPUs): MMTK_ENERGY_THREADS=2 export MMTK_ENERGY_THREADS If you want to have MMTK in Chimera use multiple CPUs always, put those lines in your .bashrc and they will apply whenever you start a new shell. --Eric On Jun 15, 2012, at 6:24 AM, A-A_lowie li wrote:
Dear Prof. Eric & other team member:
First, thanks for your reply and help. As for the platform of my computer, here is the basic information:
Ubuntu, Release 12.04 (precise) 64-bit Kernel Linux 3.2.0-24-generic GNOME 3.4.1 Intel® Core™ i7 CPU 860 @ 2.80GHz × 8 Memory:5.8G
As for the shell, i usually use bash :) Please let me know how to change the MMTK_ENERGY_THREADS parameter?
Sincerely thanks for your help.
Lowie
On Fri, Jun 15, 2012 at 1:51 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote: Hi Lowie, You don't have to install MMTK yourself. It is bundled with Chimera. Also, as this post says:
[Chimera-users] Parallel run
it depends on your platform and personal configuration. So, what platform do you use (Windows/Linux/Mac) and if it's Linux, what shell do you use?
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Jun 14, 2012, at 6:56 AM, A-A_lowie li wrote:
Dear Sir:
I am a new user of Chimera, but immediately attracted by this handy software Chimera.
Since my model requires a lot of computation time in energy minimization, could you please how to set up the environment for parallel computation of energy minimization in Chimera?
On one website, it was said, MMTK ENERGY THREADS could be reset for parallel computation.
After installation of MMTK, I am confused on how to change parameter in MMTK, and recompile Chimera (or change Chimera settings ).
Could you please give me more details about how to set MMTK ENERGY THREADS in Chimera?
Sincerely thanks for your advice.
Lowie
-- Without dream, life is incomplete! _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Without dream, life is incomplete!
perfect, thanks a lot, i will try it now :) thanks again :) On Tue, Jun 19, 2012 at 1:56 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Lowie, On Linux using bash, type this in your shell window before starting Chimera (from that same shell window) to use 2 CPUs (obviously, use a higher number if you want to use more CPUs):
MMTK_ENERGY_THREADS=2 export MMTK_ENERGY_THREADS
If you want to have MMTK in Chimera use multiple CPUs always, put those lines in your .bashrc and they will apply whenever you start a new shell.
--Eric
On Jun 15, 2012, at 6:24 AM, A-A_lowie li wrote:
Dear Prof. Eric & other team member:
First, thanks for your reply and help. As for the platform of my computer, here is the basic information:
Ubuntu, Release 12.04 (precise) 64-bit Kernel Linux 3.2.0-24-generic GNOME 3.4.1 Intel® Core™ i7 CPU 860 @ 2.80GHz × 8 Memory:5.8G
As for the shell, i usually use bash :) Please let me know how to change the MMTK_ENERGY_THREADS parameter?
Sincerely thanks for your help.
Lowie
On Fri, Jun 15, 2012 at 1:51 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Lowie, You don't have to install MMTK yourself. It is bundled with Chimera. Also, as this post says:
[Chimera-users] Parallel run<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-September/005499.html>
it depends on your platform and personal configuration. So, what platform do you use (Windows/Linux/Mac) and if it's Linux, what shell do you use?
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Jun 14, 2012, at 6:56 AM, A-A_lowie li wrote:
Dear Sir:
I am a new user of Chimera, but immediately attracted by this handy software Chimera.
Since my model requires a lot of computation time in energy minimization, could you please how to set up the environment for parallel computation of energy minimization in Chimera?
On one website, it was said, MMTK ENERGY THREADS could be reset for parallel computation.
After installation of MMTK, I am confused on how to change parameter in MMTK, and recompile Chimera (or change Chimera settings ).
Could you please give me more details about how to set MMTK ENERGY THREADS in Chimera?
Sincerely thanks for your advice.
Lowie
-- Without dream, life is incomplete! _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Without dream, life is incomplete!
-- Without dream, life is incomplete!
participants (2)
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A-A_lowie li -
Eric Pettersen