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| − | Web interface: [[WebMO]]
| + | [[Sysadmin:WebMO|Go here]] |
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| − | Users for WebMo:
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| − | * Create an LDAP user.
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| − | * [http://w0.cluster.earlham.edu/~alice/webmo-cgi-bin/login.cgi Log in] using that user's credentials
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| − | * Give the group password. (This is a one-time requirement. Future logins will not ask for it.)
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| − | * Use Gaussian.
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| − | == An old WebMO configuration example ==
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| − | [[Cluster:_New_BobSCEd_Install_Log|Notes below taken from here.]]
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| − | '''WebMO'''
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| − | * yum installed httpd
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| − | * Installed on bs0 with the following params:
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| − | <pre>
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| − | Path to perl: /usr/bin/perl
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| − | Webserver name: bs0-new.cluster.earlham.edu
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| − | HTML directory: /var/www/webmo
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| − | HTML URL: /webmo
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| − | CGI script directory: /var/www/cgi-bin
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| − | CGI script URL: /cgi-bin
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| − | User files directory: /mounts/bobsced/WebMO</pre>
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| − | * Get this error when authing with LDAP: <code>Can't locate Authen/Simple/LDAP.pm</code>
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| − | * yum installed perl-LDAP.noarch, didn't work, so used CPAN to install Authen::Simple::LDAP
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| − | * edited /var/www/cgi-bin/interfaces/authen.conf for our LDAP settings
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| − | * Before externally authenticated users can use it, you have to go in as administrator and check the box to allow them in the Webmo group (or whatever other group)
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| − | * Gamess:
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| − | ** yum install compat-gcc-34-g77.x86_64 and gfortran
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| − | ** Followed directions from [http://www.webmo.net/support/gamess_linux.html Webmo site]
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| − | * Added the following line to httpd.conf:
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| − | :<code>SuexecUserGroup bob users </code>
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| − | * Gaussian 09 not supported, though it's installed in /mounts/bobsced/usr/local/g09
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| − | * Installed g03, except get errors:
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| − | <pre>Erroneous write during file extend. write 160 instead of 4096
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| − | Probably out of disk space.
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| − | Write error in NtrExt1: No such file or directory
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| − | </pre>
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| − | or
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| − | <pre>Write error in NtrExt1: Bad address</pre>
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| − | ** To fix this, do <code>echo 0 > /proc/sys/kernel/randomize_va_space</code>
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| − | ** <font color="green">This needs to be set to happen all the time on boot</font>
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| − | == Older notes, c. 2005 ==
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| − | * [[Cluster:Gaussian environment|Gaussian environment]]
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| − | * [[Cluster:Running Gaussian in parallel|Running Gaussian in parallel]]
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| − | * [[Cluster:Gaussian PBS script|Sample Gaussian PBS script]]
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| − | === Gaussian environment ===
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| − | I use this in my .bashrc:
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| − | export GAUSS_EXEDIR=/cluster/bazaar/software/g03
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| − | export GAUSS_LFLAGS='-nodelist "b0 b1" -opt "Tsnet.Node.lindarsharg: ssh " -mp 2'
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| − | export GAUSS_SCRDIR=/tmp
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| − | export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/cluster/bazaar/software/g03
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| − | export g03root=/cluster/bazaar/software
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| − | export PATH=$PATH:/cluster/bazaar/software/g03
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| − | Seems to work, although you might want to tweak the node list.
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| − | === Running Gaussian in parallel ===
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| − | Understand the distinction between <tt>nprocs</tt> and <tt>nprocl</tt>. <tt>nprocs</tt> is for a shared-memory (single-image) machine, whereas <tt>nprocl</tt> is for a distributed-memory (cluster) system. You want to use <tt>nprocl</tt> on all our computing systems. For example, if you want to run on eight processes (four nodes), add a line like this
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| − | %nprocl=8
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| − | to your input file. You should then specify <tt>qsub -l nodes=4:ppn=2 ''script''</tt> on the command line to submit your PBS script with a requirement of four dual-processor machines.
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| − | Once you have the number of CPUs specified in the input file, make sure that your nodelist in GAUSS_LFLAGS is set properly. See [[Cluster:Gaussian_environment|Gaussian environment]] for details.
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| − | If you have a bunch of input files you want to modify, use the add_nproc.pl script in /cluster/generic/bin. First cd to the directory with your input files, and then do:
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| − | perl /cluster/generic/bin/add_nproc.pl ''n''
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| − | where ''n'' is the number proecssors you want to run on.
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| − | After that, fire it up with <tt>$g03root/bsd/g03l</tt>.
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| − | === Sample Gaussian PBS script ===
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| − | This is a sample PBS script for Gaussian:
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| − | #!/bin/sh
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| − | #PBS -N gaussian_test061.com_nodes=2:ppn=2
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| − | #PBS -o /cluster/home/skylar/bazaar/gaussian_nodes2/test061.com.out
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| − | #PBS -e /cluster/home/skylar/bazaar/gaussian_nodes2/test061.com.err
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| − | #PBS -q batch
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| − | #PBS -m abe
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| − | #PBS -l nodes=2:ppn=2
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| − | cd $PBS_O_WORKDIR
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| − | /cluster/bazaar/software/g03/bsd/g03l < /cluster/bazaar/software/g03/tests/com_smp4/test061.com > /cluster/home/skylar/bazaar/gaussian_nodes2/test061.com.log
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| − | exit $!
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