AMBER-pcluster: Difference between revisions
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=== Running Program === | === Running Program === | ||
Amber 8 | '''Amber 8''' | ||
'''Important Note''' | '''Important Note''' | ||
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Example of a shell script to run sander on the batch queue: | Example of a shell script to run sander on the batch queue: | ||
To run a serial job (serial.sh) | <u>To run a serial job</u> (serial.sh) | ||
<pre class=" | <pre class="gscript"> | ||
#!/bin/csh | #!/bin/csh | ||
cd working_directory | cd working_directory | ||
| Line 40: | Line 40: | ||
</pre> | </pre> | ||
To run a parallel job (multi.sh): | To run a parallel job (multi.sh): | ||
<pre class=" | <pre class="gscript"> | ||
#!/bin/csh | #!/bin/csh | ||
cd working_directory | cd working_directory | ||
/usr/bin/time psander -i ... | /usr/bin/time psander -i ... | ||
</pre> | </pre> | ||
'''Amber 10''' | |||
'''Important Note''' | '''Important Note''' | ||
sander is a single processor executable. A parallel version of this program is called sander.MPI. | sander is a single processor executable. A parallel version of this program is called sander.MPI. | ||
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To run a serial job (serial.sh) | To run a serial job (serial.sh) | ||
<pre class=" | <pre class="gscript"> | ||
#!/bin/bash | #!/bin/bash | ||
cd working_directory | cd working_directory | ||
| Line 58: | Line 60: | ||
/usr/local/amber10/bin/sander -i ... | /usr/local/amber10/bin/sander -i ... | ||
</pre> | </pre> | ||
To run a parallel job (multi.sh): | To run a parallel job (multi.sh): | ||
<pre class=" | <pre class="gscript"> | ||
#!/bin/bash | #!/bin/bash | ||
cd working_directory | cd working_directory | ||
| Line 65: | Line 68: | ||
poe /usr/local/amber10/bin/sander.MPI -i ... | poe /usr/local/amber10/bin/sander.MPI -i ... | ||
</pre> | </pre> | ||
For Amber 8 and Amber 10 | |||
'''For Amber 8 and Amber 10''' | |||
To submit a 10 hour long serial job to the batch queue: | To submit a 10 hour long serial job to the batch queue: | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
ugsub T1-i1-t1-10h serial.sh | |||
</pre> | </pre> | ||
To submit a 10 hour long 4-processor parallel job to the batch queue: | To submit a 10 hour long 4-processor parallel job to the batch queue: | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
ugsub T4-i4-t1-10h multi.sh | |||
</pre> | </pre> | ||
or use the following command to ensure that all 4 processors assigned are on the same node: | or use the following command to ensure that all 4 processors assigned are on the same node: | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
ambersub 4 10 multi.sh | |||
</pre> | </pre> | ||
Type llqueue at your pcluster login prompt to get more information about the batch queuenames. | Type llqueue at your pcluster login prompt to get more information about the batch queuenames. | ||
Revision as of 10:03, 13 February 2013
Category
Computational Chemistry
Program On
pcluster
Version
8,10
Author / Distributor
See http://ambermd.org , this website contains the reference(s) to use when citing Amber in the literature.
Description
Amber is a package of molecular simulation programs.
Pcluster currently has Amber 8 and Amber 10 installed. Amber 8 is the default version, which is on users’ path and by default the AMBERHOME variable is set to /usr/local/amber8.
In order to run Amber 10, users need to invoke the commands with the full path and define AMBERHOME in the script, as described below.
Running Program
Amber 8
Important Note sander is a single processor executable. A parallel version of this program is called psander.
Example of a shell script to run sander on the batch queue:
To run a serial job (serial.sh)
#!/bin/csh cd working_directory /usr/bin/time sander -i ...
To run a parallel job (multi.sh):
#!/bin/csh cd working_directory /usr/bin/time psander -i ...
Amber 10
Important Note sander is a single processor executable. A parallel version of this program is called sander.MPI.
Example of a shell script to run sander on the batch queue:
To run a serial job (serial.sh)
#!/bin/bash cd working_directory export AMBERHOME=/usr/local/amber10 /usr/local/amber10/bin/sander -i ...
To run a parallel job (multi.sh):
#!/bin/bash cd working_directory export AMBERHOME=/usr/local/amber10 poe /usr/local/amber10/bin/sander.MPI -i ...
For Amber 8 and Amber 10
To submit a 10 hour long serial job to the batch queue:
ugsub T1-i1-t1-10h serial.sh
To submit a 10 hour long 4-processor parallel job to the batch queue:
ugsub T4-i4-t1-10h multi.sh
or use the following command to ensure that all 4 processors assigned are on the same node:
ambersub 4 10 multi.sh
Type llqueue at your pcluster login prompt to get more information about the batch queuenames.
Note When a parallel job is submitted with ugsub as shown above, it is not guaranteed that all processors assigned to the job will be on the same node. If you want to ensure that all processors (up to 8) assigned to the job are on the same node (to use shared memory communication), please submit your job with ambersub instead of ugsub. Type ambersub at a pcluster command prompt to see its usage.
Documentation
User guide and documents available in /usr/local/amber8/doc/ (Amber8) and /usr/local/amber10/doc/ (Amber10)
More information at http://ambermd.org/
Installation
Amber8 is installed in /usr/local/amber8 and it is on users' default path.
Amber10 is installed in /usr/local/amber10 and it is not on users' default path.
Compiled with the IBM compilers, using MPI for the parallel versions.
AmberTools 1.2 was compiled with XLF 9.1 and gcc 3.3.2 and it is installed in /usr/local/amber10
System
64-bit Linux