Need help? Send a message to help@msi.umn.edu or call (612) 626-0802.
Gaussian03 Revision D01 has been installed and can be loaded with the command: module load g03/d01 This version is available on the altix, regatta, balt, and the x86_64 machines in the SDVL and VWL. It will become the default version of Gaussian on March 1. After that day, you can load it with: module load g03 Release notes are available at: http://www.gaussian.com/g_tech/g03_rel.htm
A bug has been found in the scheduler on the altix. The bug keeps Gaussian jobs from getting scheduled as soon as they should. Our system staff is developing a workaround for this problem. Please be patient over the next couple days if your Gaussian jobs do not start. The qg03 script was not functioning for several hours last night while some queueing changes were made. qg03 should be working now.
One of the nodes on the altix (altix2) is malfunctioning. Any Gaussian jobs scheduled on this node will die shortly after reading the input file. This node is being emptied, and it will be rebooted on Monday. Until then, the qg03 script has been modified to schedule all jobs on the a350 nodes.
1. The QuantumCube has moved to the SDVL. The QuantumCube still requires a
separate password. If you already have an SDVL account, please send an
email to help@msi.umn.edu and request a QuantumCube account. If you do
not have an SDVL account, please have your PI send an email to
accounts@msi.umn.edu with the following information:
a. Name of PI
b. Name of user
c. email address of user
d. specify that your group member wants an SDVL account and an account
on the QuantumCube.
Molpro has been installed on the QuantumCube. It can be run like this:
module load molpro
molpro h2o.com
2. GAMESS and GAMESSPLUS have been installed on the altix and on the
Power4/regatta.
The modules for GAMESS and GAMESSPLUS can be loaded with the commands:
module load gamess
module load gamessplus
To run GAMESS interactively on either of these systems, type:
rgms input.dat
To submit a GAMESS calculation to the queue, type:
qgms -m 400mb -p 4 input.dat
for help with the qgms command type:
qgms
The corresponding commands for GAMESSPLUS are:
rgmsp input.dat
and
qgmsp -m 400mb -p 4 input.dat
3. SuSE is coming.
balt.msi.umn.edu will be down in mid-november for a couple days while
the operating system is changed to SuSE Linux. The change in operating
system will resolve a number of software problems on the system. SuSE
eventually be installed on the altix, but no date has been set.
There have been several software packages recently installed. The codes
include GAMESS, Gaussian, NBO and NBOView.
1. GAMESS Nov. 22, 2004 has been installed on the regatta (power4), and sp.
It can be run in serial or parallel mode.
To use it, type:
module load gamess
to run an interactive job:
rgms example.inp
to submit a serial job to the queue:
qgms example.inp
to submit a parallel job on 4 processors to the queue:
qgms -p 4 example.inp
2. Gaussian03.b01 has been installed on the linux machines in the SDVL and
the VWL.
3. The program NBO 5.0g has been installed on nfi, regatta, and
sp. This program is a plug-in for Gaussian03 to perform bond order
calculations. The following is a list of the machine and version of
Gaussian where NBO5 is available:
machine NBO version Gaussian Version
------- ----------- ----------------
sp 5.0g g03.c01
regatta 5.0g g03.c01
nfi 5.0g g03.b01
4. The program NBOView is now available on nfi, regatta, and sp.
to run the program, type:
module load nboview
nboview
On Monday, January 7th the g98 module on ALL of the Institute machines
will be updated to point to Rev. A.11. It currently points to Rev. A.9.
If you have a project in progress that requires the use of Rev. A.9 you
will have to load the g98.a9 module instead of the g98 module.
module add g98.a9
instead of
module add g98
Rev. A.11 can be accessed by loading the g98.a11 module. On Monday,
January 7th, you will also be able to access Rev. A.11 by loading the g98
module.
Please make sure that you are aware of this change.
If you have any questions or comments please send them to
pfast@msi.umn.edu or help@msi.umn.edu.
Hello everyone.
We have installed Gaussian 98 Revision A.10 on the IBM SP. It is availabe
by loading the g98.a10 module,
module load g98.a10
Gaussian, Inc. is having problems with Revision A.10 on the SGI platforms.
We are hoping for a fix in the very near future. As soon as we have A.10
running on the SGI we will send another announcement.
Please send email to help@msi.umn.edu if you have any questions.
Hi everyone.
We have recently installed Q-Chem version 2.0 on the IBM SP. This is a
60-day trial period for this program. The demo license for Q-Chem will
expire on April 26, 2001. Please test this code thoroughly and send any
comments you have about the program to pfast@msi.umn.edu or
help@msi.umn.edu. We are trying to decide if we want to purchase the code
and your comments will help in the decision making process.
Running Q-Chem:
module add qchem
qchem input_file output_file
or
qchem input_file output_file save_dir
specifying save_dir on the command line will save any of the necessary
temporary files for a restart (orbitals, geometry, etc.). These files are
saved in the directory $QCSCRATCH/save_dir, where $QCSCRATCH is the
environment variable that designates the location for temporary files.
This can be set in your .cshrc file as
setenv QCSCRATCH /scratch1/username
where username is your personal login name and /scratch1 can also be
/scratch2. This is very similar to the $GAUSS_SCRDIR that Gaussian uses
and the Gaussian chk file. The one difference is that Q-Chem uses a
save_dir directory instead of a single chk file.
Documentation is at http://www.msi.umn.edu/software/qchem/manual_v2.0.pdf.
If you have questions please feel free to send email to pfast@msi.umn.edu
or help.msi.umn.edu.
CC-Listers.
With the recent upgrade of the IBM SP the parallel version of Gaussian
98.A.9 has broken. We are working with the Gaussian people to solve the
problem.
The serial version of A.9 is still working fine, so you can continue to
submit 1 processor jobs with A.9. (A.9 is currently the default version
of Gaussian on both the SP and the Origin)
For now parallel Gaussian jobs will have to be run with revision A.7, A.6,
or Gaussian 94. These revisions are loaded as follows:
module add g98.a7
module add g98.a6
module add g94
My current suggestion is to use A.7 in parallel as a replacement for the
broken parallel A.9. Once again, it is only the parallel portion of A.9
that is broken; A.9 still works when run with a single processor. Also,
the parallel problem with A.9 is only on the SP; A.9 is working properly
on the Origin.
We will hopefully have this fixed very soon. Please let me know if you
have any questions, pfast@msi.umn.edu or help@chem.umn.edu.
Hello everyone. Hope you had a wonderful holiday vacation.
A couple of new changes have been made that Origin users and SP-Gaussian
users will want to take note of.
Origin users:
Effective Monday, January 8, 2001 the maximum wallclock time on
the Origin will be reduced from 300 hours to 150 hours. Jobs
submitted before Monday, January 8 will be allowed to run to
completion.
If you have questions please contact me, pfast@msi.umn.edu, or
the MSI helpline, help@msi.umn.edu.
Gaussian on the IBM SP:
Effective immediately all Gaussian 94 and Gaussian 98 temporary
files, *.d2e, *.int, *.rwf, and *.scr, will be removed 14 days
(336 hours) after creation. These files are removed automatically
by Gaussian after the successful completion of a calculation;
however, these files unecessarily take up disk space after a
Gaussian calculation has crashed.
If you have questions please contact me, pfast@msi.umn.edu, or
the MSI helpline, help@msi.umn.edu.
If you have any questions about either of these changes please contact
me, pfast@msi.umn.edu, or the MSI helpline, help@msi.umn.edu.
i am in the process of coming up with tutorial topics for this spring. i would like to get input from you as to what type of tutorial would be beneficial to your research or to your research group. please get suggested topics to me by this sunday, dec. 17th. topics can be email to pfast@msi.umn.edu, or you can reach me by phone at 5-6573. this is your chance to have a voice in the tutorial planning process. i cannot guarantee that your topic will actually make the spring list, but all suggestions will be considered. thank you for the help.
We have a one month demo license for the Jaguar electronic structure
package from Schrodinger Inc. Jaguar can be used to perform HF, MP2,
LMP2, GVB, GVB-CI, and DFT calculations. Please check the documentation
for further features, www.msi.umn.edu/software/jaguar/manual.pdf or the
jaguar home page, www.schrodinger.com/jaguar2.html.
The program is only available on the IBM SP. In order to run the program
load the jaguar module,
module load jaguar
and launch the executable,
jaguar
This will start up the graphical user interface for the program.
To run Jaguar through the queue add the following to your LoadLeveler
file:
jaguar run jobname
Since this is an evaluation period please let me know if this program has
been useful in your research. If you have any questions please send email
to pfast@msi.umn.edu or to help@msi.umn.edu.
CC-Listers.
I would like to encourage Gaussian98 users to start using the qg98
script that has been created. The script has been re-written in Perl and
has some new features.
Before I go on I want stress that I am encouraging you to use the
script. This is not a requirement, simply an encouragement.
1) The script strips off any .inp, .dat, .com, .g98, or .g94 file
extensions before appending the .out, .ll, or .pbs extensions for the
output and the queue script file names.
2) The email notification has been set to 'never send email' as the
default for both the Origin and the SP. This can be changed so that email
notification is sent after a job finishes with the -e flag.
3) The script now reads the %nproc keyword in the input file to determine
the number of processors that your particular calculation needs. Remember
that the SP has a maximum number of 4 processors that can be specified.
Please see the following webpage for more details:
http://www.msi.umn.edu/software/gaussian98/details.html
From our systems point of view the qg98 script cleans up the temporary
files from crashed jobs and ensures that the correct number of processors
are being specified. From the users point of view removing crashed
temporary files allows for more useable scratch space. Checking that the
correct number of processors are being used ensures that you are getting
the resources that you expect.
If there are any questions, problems, or desired enhancements please feel
free to write to myself, pfast@msi.umn.edu, or to help@msi.umn.edu.
i have had a few questions concerning my original message about nwchem so
i thought i would clarify the details.
nwchem is now running on the sp and the origin.
on the sp:
- you can run nwchem in serial and parallel
- interactive: (only serial jobs can be run interactively)
module load nwchem
nwchem input_file > output_file
- batch:
please see www.msi.umn.edu/software/nwchem/sp-ll.html for
sample loadleveler scripts for both parallel and serial
since nwchem runs via mpi you will have to specify serial
jobs as parallel jobs in your loadlevel script. please
see the example script,
www.msi.umn.edu/software/nwchem/sp-ll.html for
clarification.
on the origin:
- you can run nwchem in serial
- interactive:
module load nwchem
nwchem input_file > output_file
- batch:
please see www.msi.umn.edu/software/nwchem/o2k-ll.html for
a sample pbs script
i hope this helps. if you have any questions please send me email at
pfast@msi.umn.edu or you can send email to help@msi.umn.edu.
nwchem has been updated to version 3.3.1 on the sp and the origin. one
major improvement is the addition of ccsd(t) energies.
the new version is available by loading the nwchem module
module load nwchem
and running the executable
nwchem input_file > output_file -- on the origin
and
nwchem input_file -proc 1 > output_file -- on the sp
if you have any questions or problems please contact me,
pfast@msi.umn.edu, or the help desk, help@msi.umn.edu.
a graphical user interface for gaussian has been installed on the sp, the
origin, and the sdvl machines. the interface is called gaussview.
-running gaussview-
load the gaussview or g98 modules
module load gaussview
or
module load g98
then run the executable gv
gv
-from the manual-
GaussView is an advanced graphical user interface designed to be
used with Gaussian to make calculations easier, quicker, and more
efficient. GaussView interface features include easy Gaussian
calclulation setup and three dimensional molecular modeling.
gaussview is a nice way to view gaussian input and output files. it has a
relativly nice molecule builder that can be used to create gaussian input
files.
currently any gaussian jobs submitted with gaussview are run interactively
on the localhost. we are working on scripts that will submit the jobs to
the queue.
note: since the gaussian program is not installed on the sdvl machines you
will not be able to submit gaussian jobs on those mahcines. rather you
will only be able to use gaussview to create input files and view input
and output files.
online documentation is available through the help menu within the
gaussview program.
if you have any problems with the gaussview program please send email to
help@msi.umn.edu.
i have installed a new molecule viewer called jmol. it is available on the sp and the origin. simply load the jmol executable: module load jmol then launch the executable: jmol this is a java program that is based off xmol.
the latest version of gaussian has now been installed on the origin 2000
and the sp. the new revision number is A.9. i will make A.9 the default
on both machines. the old versions will still be available. to use the
older version simply load the corresponding module.
A.6 -- module add g98.a6
A.7 -- module add g98.a7
A.9 -- module add g98
the scripts rg98 and qg98 have been modified on the sp to account for the
new winterhawk+ nodes. it is now possible to run gaussian via the rg98
and qg98 scripts on 4 processors. the rg98 and qg98 scripts are available
for all three version of gaussian (A.6, A.7, and A.9). simply load the
module for the version you want to use and the rg98 and qg98 scripts will
be available for that version.
the rg98 and qg98 scripts now use the environment variable GAUSS_SCRDIR to
designate the directory for the gaussian temporary files. this
environment variable should be set in your .cshrc file or in the queue
script. if it is not set the rg98 and qg98 scripts will create temporary
directories in the scratch space for the temporary files. these temporary
directories will be removed after the calculation is complete.
please check the gaussian portion of the software page on the msi website.
http://www.msi.umn.edu/user_support/software/Chemistry.html
and
http://www.msi.umn.edu/software/gaussian98/details.html
the spartan package has been updated to allow users to submit jobs to the queue. this is done by choosing the LoadLevelerQ1 option when submiting jobs. calculations can still be run interactively on the local host by choosing the localhost option when submitting jobs. this information is outlined on the msi website, http://www.msi.umn.edu/user_support/software/Chemistry.html. the link to the details page is http://www.msi.umn.edu/software/spartan/details.html. for those of you unfamiliar with the spartan package it has a really nice graphical user interface for building structures which can be used with other electronic structure packages. spartan can perform a variety of ab initio, denisty functional, semi-empirical, and molecular mechanics calculations. its a fun little program and could be very useful to your research.
This information is available in alternative formats upon request by individuals with disabilities. Please send email to alt-format@msi.umn.edu or call 612-624-0528. |
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