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informatica:hp_z400_macromodel_macromodel [2012/06/12 16:26] miquel [Gestor de cues] |
informatica:hp_z400_macromodel_macromodel [2020/07/09 12:22] miquel |
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- | ====== | + | ====== Schrödinger Suite 2012 ====== |
- | Aquest | + | La // |
+ | |||
+ | Les icones emprades indiquen, | ||
+ | * :info: - informació important per la instal·lació o configuració | ||
+ | * :ok: - pas d' | ||
+ | * :warn: - pas d' | ||
+ | * :fail: - pas d' | ||
===== Descàrrega del programa ===== | ===== Descàrrega del programa ===== | ||
Line 39: | Line 45: | ||
</ | </ | ||
- | ====== Comprovacions prèvies a la instal·lació | + | ===== Comprovacions prèvies a la instal·lació ===== |
- | ===== System requirements | + | ==== System requirements ==== |
* :ok: CPU, Memory, and Disk. En general el sistema compleix amb les especificacions recomanades. | * :ok: CPU, Memory, and Disk. En general el sistema compleix amb les especificacions recomanades. | ||
Line 54: | Line 60: | ||
* :warn: Cal modificar la configuració de xarxa a estàtica per evitar problemes si la xarxa es penja. De totes formes, com que l' | * :warn: Cal modificar la configuració de xarxa a estàtica per evitar problemes si la xarxa es penja. De totes formes, com que l' | ||
- | ===== GNU/Linux x86 64-bit executables | + | ==== GNU/Linux x86 64-bit executables ==== |
:info: La distribució Debian no és una de les que tenen suport tècnic. Tanmateix, per la seva proximitat i estreta relació amb la distribució Ubuntu, seguiré les recomanacions per aquesta distribució. | :info: La distribució Debian no és una de les que tenen suport tècnic. Tanmateix, per la seva proximitat i estreta relació amb la distribució Ubuntu, seguiré les recomanacions per aquesta distribució. | ||
Line 63: | Line 69: | ||
* :ok: On Ubuntu, symbolic links to the the libssl and libcrypto libraries must be made because of versioning differences ('' | * :ok: On Ubuntu, symbolic links to the the libssl and libcrypto libraries must be made because of versioning differences ('' | ||
- | ===== Queueing Systems | + | ==== Queueing Systems ==== |
Aquests són els gestors de cues amb què poden treballar els programes de la Schrödinger Suite. Indico quins paquets de Debian semblen correspondre al gestor de cues. En alguns casos la correspondència és clara, en altres caldrà comprovar-la. | Aquests són els gestors de cues amb què poden treballar els programes de la Schrödinger Suite. Indico quins paquets de Debian semblen correspondre al gestor de cues. En alguns casos la correspondència és clara, en altres caldrà comprovar-la. | ||
Line 78: | Line 84: | ||
* SGE version must be no earlier than 6.0u8. From 6.2u3 on, a patch or SGI reconfiguration is required if SGE preemption is used. | * SGE version must be no earlier than 6.0u8. From 6.2u3 on, a patch or SGI reconfiguration is required if SGE preemption is used. | ||
- | + | ==== Espai de disc per la instal·lació ==== | |
- | ===== Espai de disc per la instal·lació | + | |
Tenint present els requisits, | Tenint present els requisits, | ||
- | < | + | |
Disk space requirements for a full installation of Schrödinger software, including the documentation, | Disk space requirements for a full installation of Schrödinger software, including the documentation, | ||
</ | </ | ||
Line 95: | Line 100: | ||
</ | </ | ||
- | ===== Maestro 9.3 Requirements | + | ==== Maestro 9.3 Requirements ==== |
Aquest són els requisits específics del programa Maestro v. 9.3, | Aquest són els requisits específics del programa Maestro v. 9.3, | ||
Line 105: | Line 110: | ||
* :ok: PDF reader. For Adobe Reader a version no earlier than 7.0.5 is recommended. La versió d' | * :ok: PDF reader. For Adobe Reader a version no earlier than 7.0.5 is recommended. La versió d' | ||
- | ===== Notes sobres els productes | + | ==== Notes sobres els productes ==== |
Per ara em salto aquesta secció (//2.4 Product Notes//), ja que caldrà veure primer quins programes s' | Per ara em salto aquesta secció (//2.4 Product Notes//), ja que caldrà veure primer quins programes s' | ||
- | ===== Verifying System Compliance | + | ==== Verifying System Compliance ==== |
Faig servir la comanda '' | Faig servir la comanda '' | ||
Line 138: | Line 143: | ||
</ | </ | ||
- | ====== Instal·lació de la Schrödinger Suite ====== | + | ===== Instal·lació de la Schrödinger Suite ===== |
:info: La instal·lació la faig com a usuari root (sudo -s). | :info: La instal·lació la faig com a usuari root (sudo -s). | ||
- | ===== Scracth disk ===== | + | ==== Scracth disk ==== |
Abans de començar, creo la carpeta /// | Abans de començar, creo la carpeta /// | ||
- | ===== ./ | + | ==== ./INSTALL ==== |
Aquesta és la sessió d' | Aquesta és la sessió d' | ||
- | ==== Inici ==== | + | === Inici === |
La primera pantalla ens proporciona unes breus instruccions d'ús del programa d' | La primera pantalla ens proporciona unes breus instruccions d'ús del programa d' | ||
Line 174: | Line 179: | ||
</ | </ | ||
- | ==== On instal·lar el programa? | + | === On instal·lar el programa? === |
A la pantalla següent, se'ns demana ón instal·lar el programa. Si el directori no existeix, ens pregunta si el volem crear. A GNU/Linux, el [[wp> | A la pantalla següent, se'ns demana ón instal·lar el programa. Si el directori no existeix, ens pregunta si el volem crear. A GNU/Linux, el [[wp> | ||
Line 202: | Line 207: | ||
</ | </ | ||
- | ==== Hardware/ | + | === Hardware/ |
El programa d' | El programa d' | ||
Line 228: | Line 233: | ||
</ | </ | ||
- | ==== Selecció de mòduls | + | === Selecció de mòduls === |
En aquest apartat, el programa d' | En aquest apartat, el programa d' | ||
Line 313: | Line 318: | ||
</ | </ | ||
- | ==== Directori " | + | === Directori " |
Aquest és el directori que hem creat més amunt i que està a disposició dels programes de càlcul per guardar fitxers temporals, | Aquest és el directori que hem creat més amunt i que està a disposició dels programes de càlcul per guardar fitxers temporals, | ||
Line 344: | Line 349: | ||
</ | </ | ||
- | ==== Resum de les opcions d' | + | === Resum de les opcions d' |
Aquesta pantalla resumeix els mòduls que s' | Aquesta pantalla resumeix els mòduls que s' | ||
Line 371: | Line 376: | ||
</ | </ | ||
- | ==== Fitxer ' | + | === Fitxer ' |
El pas següent és comprovar el contingut del fitxer // | El pas següent és comprovar el contingut del fitxer // | ||
Line 440: | Line 445: | ||
* processors - a les instruccions d' | * processors - a les instruccions d' | ||
- | ==== Licensing | + | === Licensing === |
En aquesta pantalla apareix la informació necessària (machine name, host id) per sol·licitar la llicència. | En aquesta pantalla apareix la informació necessària (machine name, host id) per sol·licitar la llicència. | ||
Line 471: | Line 476: | ||
</ | </ | ||
- | ==== Finalment... la instal·lació | + | === Finalment... la instal·lació === |
Després de prémer el botó < | Després de prémer el botó < | ||
Line 482: | Line 487: | ||
Per ara, l' | Per ara, l' | ||
- | ===== Espai de disc ocupat | + | ==== Espai de disc ocupat ==== |
Un cop finalitzada la instal·lació, | Un cop finalitzada la instal·lació, | ||
Line 490: | Line 495: | ||
* 252 MiB ./ | * 252 MiB ./ | ||
* 1585 MiB ./ | * 1585 MiB ./ | ||
+ | |||
+ | ===== Instal·lació i activació de la llicència ===== | ||
+ | |||
+ | Aquest és el contingut del correu electrònic amb la llicència i instruccions per instal·lar-la. Per motius de seguretat, els noms de persones han estat substituïts per inicials, i les dades de la llicència han estat eliminades. També he esborrat la part relativa a clústers d' | ||
+ | |||
+ | < | ||
+ | Thank you for your purchase, K.D. has asked us to make the end date 1 year from today. | ||
+ | |||
+ | Attached and listed below are the license files which will enable access to 1 job of MacroModel with Confgen as well as access to KNIME and Maestro. **These licenses are served from your new Linux machine called cie-48-184.uab.es and are valid through 12-Jun-2013.** | ||
+ | |||
+ | To activate these, replace the current " | ||
+ | < | ||
+ | $SCHRODINGER/ | ||
+ | </ | ||
+ | (not wrapped and exactly as shown) on cie-48-184 to activate the license server daemon. | ||
+ | |||
+ | Once the licenser server is active you should have no problems running the Schrodinger products. | ||
+ | |||
+ | If you encounter any errors please use the 2012 Diagnostics Tool. To run the diagnostics tool please enter $SCHRODINGER/ | ||
+ | |||
+ | If the license server is on a remote machine and you are encountering errors, you should run the following five steps on both the license server and on your local machine: | ||
+ | |||
+ | First - Open a terminal window. | ||
+ | |||
+ | Second - Set the SCHRODINGER environment variable to point to your software installation. | ||
+ | |||
+ | Third - Enter the command $SCHRODINGER/ | ||
+ | |||
+ | When the licadmin program finishes, it prints a message telling you the name of the file it created. The name is in the form username-machine-license-info.tar.gz. This file should be in the current directory. | ||
+ | |||
+ | Fourth - Rename the file to username-machine-license-info.tarball. This is necessary because some mail programs filter out files with a .tar.gz extension. | ||
+ | |||
+ | Finally - Send the renamed file to help@schrodinger.com. | ||
+ | |||
+ | If you have other questions or problems please see our online knowledge base at: http:// | ||
+ | |||
+ | If there is anything else we can do for you please let us know. | ||
+ | |||
+ | Sincerely, | ||
+ | |||
+ | Kimberly Lehmann | ||
+ | |||
+ | **Please send only license requests to licensing@schrodinger.com. All other questions or queries should go to help@schrodinger.com. Thank you.** | ||
+ | |||
+ | # Date generated: <Tue Jun 12 14:51:41 PDT 2012> | ||
+ | # Server flexid: | ||
+ | # ... | ||
+ | |||
+ | ---------------------------------------------------------------------- | ||
+ | Schrodinger Licensing | licensing@schrodinger.com | ||
+ | http:// | ||
+ | 101 SW Main Street, Suite 1300, Portland, OR 97204 | ||
+ | ---------------------------------------------------------------------- | ||
+ | Find answers in our searchable Knowledge Base! | ||
+ | | ||
+ | ---------------------------------------------------------------------- | ||
+ | |||
+ | </ | ||
+ | |||
+ | ==== License Installation Instructions ==== | ||
+ | |||
+ | The instructions below assume that the SCHRODINGER environment variable has been set to the directory where you have installed the software. | ||
+ | |||
+ | |||
+ | === Editing the license file === | ||
+ | |||
+ | 1. Add the license information that was sent to you to the end of your $SCHRODINGER/ | ||
+ | |||
+ | 2. Close and save the changes to the license file. Please ensure that the license file has the appropriate read permissions. | ||
+ | |||
+ | 3. If your license file does not contain a SERVER line, and does not have any FEATURE or INCREMENT sections specifying HOSTID=INTERNET=, | ||
+ | |||
+ | If your license file does not contain a SERVER line, but *does* have FEATURE or INCREMENT sections specifying HOSTID=INTERNET=, | ||
+ | |||
+ | 4. If your license file *does* contain a SERVER line, you will need to either start the Schrodinger-installed license server daemon for the first time, or make the currently-running copy of the Schrodinger-installed license server daemon reread the license file. | ||
+ | |||
+ | If you are installing the license information for the first time, and have not previously started the license server daemon using the licensing software installed with your Schrodinger software, please proceed to the section titled " | ||
+ | |||
+ | If you edit the license file after having already started the license server daemon (lmgrd) using the Schrodinger-installed licensing software, you will need to tell lmgrd to reread the updated license file. This is usually the case if you have added additional license lines to your file that already contained license information. | ||
+ | |||
+ | If you encounter any problems, please see the Troubleshooting sectionbelow. | ||
+ | |||
+ | |||
+ | === Rereading the license file === | ||
+ | |||
+ | You can instruct an already-running instance of the Schrodinger-installed license server daemon to reread the license file by executing the following command: | ||
+ | < | ||
+ | $SCHRODINGER/ | ||
+ | </ | ||
+ | Please execute this command each time you add new lines to the license file and wish to have the updated license information read by an already-running copy of the license server daemon. | ||
+ | |||
+ | After executing a reread, you may want to check the current status of available licenses with the following command: | ||
+ | < | ||
+ | $SCHRODINGER/ | ||
+ | </ | ||
+ | |||
+ | === Starting the license server daemon (lmgrd) === | ||
+ | |||
+ | 1. Before starting the license server daemon, you should set your FLEXLM_DIAGNOSTICS environment variable to 3, which will provide the highest level of license debugging output. This additional output can be used to troubleshoot any problems you may experience with starting the license server. | ||
+ | |||
+ | For bash or ksh, FLEXLM_DIAGNOSTICS can be set with the following command: | ||
+ | < | ||
+ | export FLEXLM_DIAGNOSTICS=3 | ||
+ | </ | ||
+ | |||
+ | For csh, FLEXLM_DIAGNOSTICS can be set with the following command: | ||
+ | < | ||
+ | setenv FLEXLM_DIAGNOSTICS 3 | ||
+ | </ | ||
+ | |||
+ | (* Once you've verified that the license server has started and everything is working correctly, you can unset your FLEXLM_DIAGNOSTICS environment variable if you wish. This may be desirable if you have other software running which also uses FLEXlm, as they will also produce additional debugging output as long as this environment variable is set.) | ||
+ | |||
+ | 2. If your license file contains a SERVER line, and you have not already previously started the license server, then execute the command: | ||
+ | < | ||
+ | $SCHRODINGER/ | ||
+ | </ | ||
+ | (exactly as shown). This command will start lmgrd, the license server daemon. lmgrd will listen for license requests on the port designated by the third argument after the word SERVER on the SERVER line of the license file. | ||
+ | |||
+ | For example, in the following SERVER line: | ||
+ | < | ||
+ | SERVER lsnode b0019732 27000 | ||
+ | </ | ||
+ | 27000 is the port on which the machine lsnode will listen for license requests. | ||
+ | |||
+ | If no port is specified on the SERVER line, a default port in the range 27000-27009 is used. | ||
+ | |||
+ | 3. Available command-line arguments for the licadmin utility may be viewed with the command: | ||
+ | < | ||
+ | $SCHRODINGER/ | ||
+ | </ | ||
+ | |||
+ | === Setting up client machines === | ||
+ | |||
+ | 1. To allow client machines to access license information from the license server, the LM_LICENSE_FILE environment variable must be set appropriately on the client machines. | ||
+ | |||
+ | For bash or ksh, FLEXLM_DIAGNOSTICS can be set with: | ||
+ | < | ||
+ | export FLEXLM_DIAGNOSTICS=3 | ||
+ | </ | ||
+ | |||
+ | For csh, FLEXLM_DIAGNOSTICS can be set with: | ||
+ | < | ||
+ | setenv FLEXLM_DIAGNOSTICS 3 | ||
+ | </ | ||
+ | |||
+ | Before attempting to set the LM_LICENSE_FILE variable, please check whether it has already been set to a particular value by executing the command: | ||
+ | < | ||
+ | echo $LM_LICENSE_FILE | ||
+ | </ | ||
+ | If the command above returns no output, then the LM_LICENSE_FILE variable has not yet been set. | ||
+ | |||
+ | If the LM_LICENSE_FILE environment variable has not been set, it can be set as follows: | ||
+ | |||
+ | For bash or ksh, LM_LICENSE_FILE can be set with the following command: | ||
+ | < | ||
+ | export LM_LICENSE_FILE=[port]@< | ||
+ | </ | ||
+ | For csh, LM_LICENSE_FILE can be set with the following command: | ||
+ | < | ||
+ | setenv LM_LICENSE_FILE [port]@< | ||
+ | </ | ||
+ | If the echo $LM_LICENSE_FILE command shows that the LM_LICENSE_FILE environment variable has already been set, then new values can be appended with the following commands: | ||
+ | |||
+ | For bash or ksh, a new value can be appended to LM_LICENSE_FILE with the following command: | ||
+ | < | ||
+ | export LM_LICENSE_FILE=[port]@< | ||
+ | </ | ||
+ | For csh, a new value can be appended to LM_LICENSE_FILE with the following command: | ||
+ | < | ||
+ | setenv LM_LICENSE_FILE [port]@< | ||
+ | </ | ||
+ | |||
+ | In all the commands above, replace < | ||
+ | |||
+ | === Enabling license communication across a firewall or proxy === | ||
+ | |||
+ | If the client machine and the license server are separated by a firewall or proxy, it will probably be necessary to specify a port on the VENDOR line of the license in order to enable license communication. Any unused port may be chosen, but the port specified will need to be made available on the firewall or proxy. | ||
+ | < | ||
+ | SERVER lsnode b0019732 27000 | ||
+ | VENDOR SCHROD PORT=10081 | ||
+ | </ | ||
+ | and the client machine and license server are separated by a firewall or proxy, then ports 27000 and 10081 will need to be made available to the client. | ||
+ | |||
+ | |||
+ | |||
===== Configuració ===== | ===== Configuració ===== | ||
Line 495: | Line 685: | ||
El pas següent és configurar el sistema i els comptes dels usuaris per tal que puguin cridar i executar correctament els programes instal·lats. | El pas següent és configurar el sistema i els comptes dels usuaris per tal que puguin cridar i executar correctament els programes instal·lats. | ||
+ | ==== Variables d' | ||
+ | Variables de entorn, | ||
+ | * Afegeixo la carpeta on està instal·lat el programa a la variable PATH. | ||
+ | * Per ara no faig ús d' | ||
+ | * Per ara no defineixo '' | ||
+ | * Per ara no defineixo '' | ||
+ | * Defineixo '' | ||
+ | |||
+ | Per simplicitat, | ||
+ | < | ||
+ | # schrodinger.sh - created by MCE for SCHRODINGER SUITE 2012 | ||
+ | PATH=/ | ||
+ | export SCHRODINGER=/ | ||
+ | # export PYTHONPATH= | ||
+ | # export SCHRODINGER_PYTHONPATH= | ||
+ | # export PYMOLMAESTRO= | ||
+ | export SCHRODINGER_HELP_BROWSER=/ | ||
+ | export SCHRODINGER_PDF_VIEWER=/ | ||
+ | </ | ||
+ | i '' | ||
+ | < | ||
+ | # schrodinger.csh - created by MCE for SCHRODINGER SUITE 2012 | ||
+ | setenv PATH / | ||
+ | setenv SCHRODINGER / | ||
+ | # setenv PYTHONPATH | ||
+ | # setenv SCHRODINGER_PYTHONPATH | ||
+ | # setenv PYMOLMAESTRO | ||
+ | setenv SCHRODINGER_HELP_BROWSER / | ||
+ | setenv SCHRODINGER_PDF_VIEWER / | ||
+ | </ | ||
+ | |||
+ | |||
+ | |||
+ | |||
+ | |||
+ | |||
+ | |||
+ | ===== Testing the installation ===== | ||
+ | |||
+ | < | ||
+ | # / | ||
+ | ------------------------------------------------------------------------ | ||
+ | Schrodinger installation check (rev 1.31) | ||
+ | ------------------------------------------------------------------------ | ||
+ | |||
+ | Test files will be written in directory instcheck-cie-48-184-4fdb5e50/ | ||
+ | |||
+ | Hosts file: / | ||
+ | |||
+ | There is only 1 host entry in this file. | ||
+ | * There are NO host entries for running immediate jobs on remote machines. | ||
+ | * There are NO host entries for submitting batch jobs. | ||
+ | |||
+ | |||
+ | ------------------------------------------------------------------------------------------ | ||
+ | Schrodinger Installation Check (rev 1.31) | ||
+ | ------------------------------------------------------------------------------------------ | ||
+ | |||
+ | Hosts file: / | ||
+ | |||
+ | ****** | ||
+ | ****** | ||
+ | ****** | ||
+ | |||
+ | ------------------ -------------------- ------- | ||
+ | Hosts Entry Check Result | ||
+ | ------------------ -------------------- ------- | ||
+ | localhost | ||
+ | ------------------------------------------------------------------------------------------ | ||
+ | |||
+ | This table can also be found in the file instcheck-cie-48-184-4fdb5e50.summary . | ||
+ | See that file for additional comments on any issues identified above. | ||
+ | |||
+ | The output files and other results of these tests have been archived in the | ||
+ | following file: | ||
+ | ... | ||
+ | </ | ||
+ | |||
+ | < | ||
+ | # / | ||
+ | ------------------------------------------------------------------------ | ||
+ | Schrodinger installation check (rev 1.31) | ||
+ | ------------------------------------------------------------------------ | ||
+ | |||
+ | Test files will be written in directory instcheck-cie-48-184-4fdb5f04/ | ||
+ | |||
+ | Hosts file: / | ||
+ | |||
+ | There is only 1 host entry in this file. | ||
+ | * There are NO host entries for running immediate jobs on remote machines. | ||
+ | * There are NO host entries for submitting batch jobs. | ||
+ | |||
+ | 1 test job will be launched. | ||
+ | |||
+ | Progress will be logged in instcheck-cie-48-184-4fdb5f04/ | ||
+ | |||
+ | This may take 15 minutes or more - please be patient. | ||
+ | A summary of the results will be given when all jobs are done. | ||
+ | |||
+ | ------------------------------------------------------------------------------------------ | ||
+ | Schrodinger Installation Check (rev 1.31) | ||
+ | ------------------------------------------------------------------------------------------ | ||
+ | |||
+ | Hosts file: / | ||
+ | |||
+ | ------------------ -------------------- ------- | ||
+ | Hosts Entry Check Result | ||
+ | ------------------ -------------------- ------- | ||
+ | localhost | ||
+ | ------------------------------------------------------------------------------------------ | ||
+ | |||
+ | This table can also be found in the file instcheck-cie-48-184-4fdb5f04.summary . | ||
+ | See that file for additional comments on any issues identified above. | ||
+ | |||
+ | The output files and other results of these tests have been archived in the | ||
+ | following file: | ||
+ | |||
+ | Archive: instcheck-cie-48-184-4fdb5f04.tarball | ||
+ | |||
+ | If you need help understanding any of these results, please send | ||
+ | this file to help@schrodinger.com, | ||
+ | |||
+ | |||
+ | Done. | ||
+ | </ | ||
===== Gestor de cues ===== | ===== Gestor de cues ===== | ||
Line 528: | Line 843: | ||
* ... | * ... | ||
+ | ===== Running Maestro ===== | ||
+ | |||
+ | Després d'un primer missatge d' | ||
+ | < | ||
+ | sermn-uab@cie-48-184: | ||
+ | License file: / | ||
+ | Log file: lmgrd.cie-48-184.log | ||
+ | sermn-uab@cie-48-184: | ||
+ | 4780 pts/0 S 0:00 / | ||
+ | 4781 ? Ssl 0:00 SCHROD -T cie-48-184 11.10 3 -c / | ||
+ | 4785 pts/0 S+ 0:00 grep lice | ||
+ | </ | ||
+ | i provo a executar el programa //Maestro// | ||
+ | < | ||
+ | sermn-uab@cie-48-184: | ||
+ | </ | ||
+ | i s' | ||
+ | {{: | ||
+ | |||
+ | <WRAP important> | ||
+ | Caldrà comprovar perquè el gestor de llicències no s'ha posat en marxa automàticament. Per ara, sembla ser que no hi ha cap //script// a /// | ||
+ | </ | ||
+ | Per començar trio el perfil per defecte: //Maestro// i finalment s'obre la finestra principal del programa. | ||