Schrodinger notes

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SCHRODINGER - getting it running

Get a License File:

Get an email about Schrodinger license keys ready for retrieval.
Click the link that follows: "please use this form to generate the license file:"

In the License Retrieval Assistant, make sure you have the following information for the respective categories:
Host ID: 0015605f526c
Machine Name: nis.compbio.ucsf.edu
FLEXIm Server Port: 2700

Debugging:

Cluster 0, all schrodinger files are located locally on nfshead2:/raid3 but the commands below should be executed on nis as user tdemers.

Make sure that the variable $LM_LICENSE_FILE has port@same_exact_server_name_as_in_license_file. The license.dat file must contain:

SERVER nis.compbio.ucsf.edu 0015605f526c 27000
VENDOR SCHROD PORT=53000

Make sure the port is open in iptables

source /raid3/software/schrodinger/current.sh 

Try some combination of the following:

$SCHRODINGER/licadmin STAT -c $SCHRODINGER/license.dat
$SCHRODINGER/licadmin REREAD -l $SCHRODINGER/lmgrd.log -c $SCHRODINGER/license.dat
$SCHRODINGER/licadmin SERVERDOWN
$SCHRODINGER/licadmin SERVERUP -l $SCHRODINGER/lmgrd.log -c $SCHRODINGER/license.dat

Installing Schrodinger on Cluster 0

First you need to go to the website and download the software. You should end up with two files: Schrodinger Worflow … .zip and Schrodinger Suites …..tar scp both these files to the server, to the schrodinger directory. On the server, in the schrodinger directory mkdir MonthYear. cd into that directory Untar the tar file and run the INSTALL script. At the end you’ll see something like this:

*) Licensing
   You will need one or more licenses before you can run the
   software you have just installed. 
Please note the following information, which you will need in order to generate a license key:
Host ID: 001e0bd543b8 Machine name: nfshead2.bkslab.org
If you are not performing this installation on your license server, you will need the output of:
$SCHRODINGER/machid -hostid

Installing Schrodinger 2019 on Cluster 2

https://www.schrodinger.com/downloads/releases

Select the Linux 64-bit version. Download it to your local computer first. Then scp the tarball over the nfs-soft in the appropriate directory. Extract the tarball and you'll get a bunch of smaller tarfiles.

# ls
Schrodinger_Suites_2019-1_Linux-x86_64.tar
# tar -xvf Schrodinger_Suites_2019-1_Linux-x86_64.tar 
Schrodinger_Suites_2019-1_Linux-x86_64/canvas-v3.9-Linux-x86_64.tar.gz
Schrodinger_Suites_2019-1_Linux-x86_64/mcpro-v5.3-Linux-x86_64.tar.gz
Schrodinger_Suites_2019-1_Linux-x86_64/desmond-v5.7-Linux-x86_64.tar.gz
Schrodinger_Suites_2019-1_Linux-x86_64/INSTALL
Schrodinger_Suites_2019-1_Linux-x86_64/SchrodingerKNIMEUpdateSite_4.5.11.201902112207.zip
Schrodinger_Suites_2019-1_Linux-x86_64/alldocs-v4.5-docs.tar.gz
Schrodinger_Suites_2019-1_Linux-x86_64/maestro-v11.9-Linux-x86_64.tar.gz
Schrodinger_Suites_2019-1_Linux-x86_64/mmshare-v4.5-Linux-x86_64.tar.gz
Schrodinger_Suites_2019-1_Linux-x86_64/macromodel-v12.3-Linux-x86_64.tar.gz
Schrodinger_Suites_2019-1_Linux-x86_64/psp-homology-thirdparty-databases.tar.gz
Schrodinger_Suites_2019-1_Linux-x86_64/combiglide-v5.2-Linux-x86_64.tar.gz
Schrodinger_Suites_2019-1_Linux-x86_64/psp-v5.5-Linux-x86_64.tar.gz
Schrodinger_Suites_2019-1_Linux-x86_64/knime-v4.5-Linux-x86_64.tar.gz
Schrodinger_Suites_2019-1_Linux-x86_64/epik-v4.7-Linux-x86_64.tar.gz
Schrodinger_Suites_2019-1_Linux-x86_64/aacg-v2.7-Linux-x86_64.tar.gz
Schrodinger_Suites_2019-1_Linux-x86_64/jaguar-v10.3-Linux-x86_64.tar.gz
Schrodinger_Suites_2019-1_Linux-x86_64/impact-v8.2-Linux-x86_64.tar.gz
Schrodinger_Suites_2019-1_Linux-x86_64/glide-v8.2-Linux-x86_64.tar.gz
Schrodinger_Suites_2019-1_Linux-x86_64/qikprop-v5.9-Linux-x86_64.tar.gz
Schrodinger_Suites_2019-1_Linux-x86_64/bioluminate-v3.4-Linux-x86_64.tar.gz
Schrodinger_Suites_2019-1_Linux-x86_64/pldb-v4.5-Linux-x86_64.tar.gz
Schrodinger_Suites_2019-1_Linux-x86_64/EULA.rtf
Schrodinger_Suites_2019-1_Linux-x86_64/CHECKSUM.md5

https://www.schrodinger.com/license-installation-instructions

We do not need to untar these individually. The INSTALL script takes care of nearly everything. All we have to do is set the path of where we want the installed programs to go to.

[root@bet ~]# export SCHRODINGER=/export/soft/schrodinger/2019-1/
[root@bet ~]# ./INSTALL