Difference: Palma:tipps:english (1 vs. 8)

Revision 82018-05-28 - HolgerAngenent

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META TOPICPARENT name="PALMA:english"

Tips und Tricks for Palma

Export directories for other user via ACL

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Sometimes, access to your files should be granted to other users. If they are not member of your own group, the directory has to be made world-readable. A more fine granular access control can be realized with so-called ACLs. The commands "getfacl" and "setfacl" enable it to give individual users read and write permissions to specific files. A detailed description of these commands can be found here: ACL with Linux.
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Sometimes, access to your files should be granted to other users. If they are not member of your own group, the directory has to be made world-readable. A more fine granular access control can be realized with so-called ACLs. The commands "getfacl" and "setfacl" enable it to give individual users read and write permissions to specific files. A detailed description of these commands can be found here: ACL with Linux.
 

I want to login from different computers to palma and do not want to open serveral ssh-connections every time

Revision 72013-10-11 - MartinLeweling

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META TOPICPARENT name="PALMA:english"

Tips und Tricks for Palma

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Why is my MPI program that slow?

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MPI programs are sometimes slowed down by too many communication. Tools like the Intel Trace Analyzer will help to determine this. If you use Intel-MPI, just load the module "intel/itac" and link the code with the switch "-trace":
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MPI programs are sometimes slowed down by too much communication. Tools like the Intel Trace Analyzer will help to determine this. If you use Intel-MPI, just load the module "intel/itac" and link the code with the switch "-trace":
 
module add intel/mpi
Line: 45 to 45
 
  • showbf -c queue: Shows the number of cores that is available immediately and for how long this is the case. Example: showbf -c default

There are many free nodes, why does my job does not run?

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This can be the case due to the fact that not every node is not member of every queue. Some nodes can be used exclusively by some workgroups, so their ressources cannot be used by everyone.
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This can be the case due to the fact that not every node is a member of every queue. Some nodes can be used exclusively by some workgroups, so their ressources cannot be used by everyone.

Revision 62013-02-19 - HolgerAngenent

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META TOPICPARENT name="PALMA:english"

Tips und Tricks for Palma

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  • showstart jobid: Shows an estimation, when a job will start. Only usable, as long as it is not running.
  • checkjob [-v] jobid : Gives some properties about your job. With the switch -v, a detailed view for every node is shown, if it is feasible to start your job.
  • showq: Show running, idle and blocked jobs. Jobs can be blocked due to limitations like when you have too many other jobs running at the same time
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  • showbf -c queue: Shows the number of cores that is available immediately and for how long this is the case. Example: showbf -c default

There are many free nodes, why does my job does not run?

This can be the case due to the fact that not every node is not member of every queue. Some nodes can be used exclusively by some workgroups, so their ressources cannot be used by everyone.

Revision 52012-12-05 - HolgerAngenent

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META TOPICPARENT name="PALMA:english"

Tips und Tricks for Palma

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Freigeben von Verzeichnissen für andere Nutzer per ACL

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Export directories for other user via ACL

 
Changed:
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Sometimes, acces to your files should be granted to other users. If they are not member of your own group, the directory has to be made world-readable. A more fine granular acces control can be realized with so-calles ACLs. The commands "getfacl" and "setfacl" enable it to give individual users read and write permissions to specific files. A detailed description of these commands can be found here: ACL with Linux.
>
>
Sometimes, access to your files should be granted to other users. If they are not member of your own group, the directory has to be made world-readable. A more fine granular access control can be realized with so-called ACLs. The commands "getfacl" and "setfacl" enable it to give individual users read and write permissions to specific files. A detailed description of these commands can be found here: ACL with Linux.
 

I want to login from different computers to palma and do not want to open serveral ssh-connections every time

Line: 28 to 28
  The complete manual can be found here.
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-- HolgerAngenent - 2010-08-16
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Access to files in your home directory via sshfs

If you want to mount your PALMA home-directory on your (Linux-) desktop PC, you can do this via sshfs. HowTos can be found here:

Some hints regarding the batch system

There are some commands that can tell you more about the jobs enqueued in the batch system

  • showstart jobid: Shows an estimation, when a job will start. Only usable, as long as it is not running.
  • checkjob [-v] jobid : Gives some properties about your job. With the switch -v, a detailed view for every node is shown, if it is feasible to start your job.
  • showq: Show running, idle and blocked jobs. Jobs can be blocked due to limitations like when you have too many other jobs running at the same time

Revision 42012-06-15 - HolgerAngenent

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META TOPICPARENT name="PALMA:english"

Tips und Tricks for Palma

Added:
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Freigeben von Verzeichnissen für andere Nutzer per ACL

Sometimes, acces to your files should be granted to other users. If they are not member of your own group, the directory has to be made world-readable. A more fine granular acces control can be realized with so-calles ACLs. The commands "getfacl" and "setfacl" enable it to give individual users read and write permissions to specific files. A detailed description of these commands can be found here: ACL with Linux.

 

I want to login from different computers to palma and do not want to open serveral ssh-connections every time

In this case use the Login via vnc. Even after closing the vncviewer, the session remains open.

Revision 32011-11-07 - HolgerAngenent

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META TOPICPARENT name="PALMA:english"
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Tipps und Tricks zur Benutzung von Palma

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Tips und Tricks for Palma

 
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Ich möchte mich von verschiedenen Rechnern aus auf Palma einloggen und es stört, immer die ganzen ssh-Verbindungen neu zu öffnen

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I want to login from different computers to palma and do not want to open serveral ssh-connections every time

 
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In diesem Fall macht der Login über vnc Sinn. Auch beim Schließen des vncviewers bleibt die Sitzung erhalten.
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In this case use the Login via vnc. Even after closing the vncviewer, the session remains open.
 
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Warum läuft mein MPI-Programm so langsam?

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Why is my MPI program that slow?

MPI programs are sometimes slowed down by too many communication. Tools like the Intel Trace Analyzer will help to determine this. If you use Intel-MPI, just load the module "intel/itac" and link the code with the switch "-trace":

 
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Wenn der Verdacht besteht, das das Programm zu viel Zeit mit Kommunikation verbraucht, kann mit dem Intel Trace Analyzer eine grafische Analyse vorgenommen werden. Dazu ist es im Fall vom Intel-MPI nur nötig, das modul "intel/itac" zu laden und beim Linken des Programms den Schalter "-trace" zu setzen. Beispiel:
 
module add intel/mpi
module add intel/itac
mpiicpc -o democode democode.cpp -trace -O3
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Das Programm wird jetzt wie üblich über das Batch-System ausgeführt. Wenn es beendet ist, liegen im Verzeichnis diverse Dateien mit der Endung .stf.* Um diese auszuwerten muss der traceanalyzer aufgerufen werden.
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Execute the program as usual via the batch-system. After finishing the run, there are different files with the suffix .stf.*. These can by analyzed with the traceanalyzer:
 
traceanalyzer Programmname.stf
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Da das Programm eine grafische Ausgabe hat, muss beim Öffnen der ssh-Verbindung das X-forwarding eingeschaltet werden. Unter Linux dazu mit "ssh -X" verbinden, unter Windows und beispielsweise putty muss der Haken beim "Enable X11-forwarding" gesetzt werden.

Das ausführliche Handbuch gibt es hier.

Intel C, C++ oder Fortran Compiler: Das Linken von Bibliotheken schlägt fehl

Dies kann vorkommen, wenn gegen Systembibliotheken gelinkt wird (z.B. libX11, libpthread,...). Dafür kann es verschiedene Gründe geben:

  • Überprüfen Sie, ob alle benötigten Bibliotheken angeben wurden.
  • 32 Bit Objekte können nicht mit 64 bit ausführbare Dateien verlinkt werden.
  • Statt -static kann es helfen, den Schalter -i-static zu verwenden. In diesem Fall werden nur die Intel Bibliotheken statisch verlinkt.
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Because of the GUI, you have to enable the X-forwarding while establishing the ssh connection (and start a local X-server like xming, if you run Windows). In Linux, use the switch -X, in putty, you habe to "Enable X11-forwarding".
 
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The complete manual can be found here.
  -- HolgerAngenent - 2010-08-16 \ No newline at end of file

Revision 22010-08-17 - HolgerAngenent

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META TOPICPARENT name="PALMA:english"
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Tipps und Tricks zur Benutzung von Palma

 
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Ich möchte mich von verschiedenen Rechnern aus auf Palma einloggen und es stört, immer die ganzen ssh-Verbindungen neu zu öffnen

 
Added:
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In diesem Fall macht der Login über vnc Sinn. Auch beim Schließen des vncviewers bleibt die Sitzung erhalten.

Warum läuft mein MPI-Programm so langsam?

Wenn der Verdacht besteht, das das Programm zu viel Zeit mit Kommunikation verbraucht, kann mit dem Intel Trace Analyzer eine grafische Analyse vorgenommen werden. Dazu ist es im Fall vom Intel-MPI nur nötig, das modul "intel/itac" zu laden und beim Linken des Programms den Schalter "-trace" zu setzen. Beispiel:

module add intel/mpi
module add intel/itac
mpiicpc -o democode democode.cpp -trace -O3

Das Programm wird jetzt wie üblich über das Batch-System ausgeführt. Wenn es beendet ist, liegen im Verzeichnis diverse Dateien mit der Endung .stf.* Um diese auszuwerten muss der traceanalyzer aufgerufen werden.

traceanalyzer Programmname.stf
Da das Programm eine grafische Ausgabe hat, muss beim Öffnen der ssh-Verbindung das X-forwarding eingeschaltet werden. Unter Linux dazu mit "ssh -X" verbinden, unter Windows und beispielsweise putty muss der Haken beim "Enable X11-forwarding" gesetzt werden.

Das ausführliche Handbuch gibt es hier.

Intel C, C++ oder Fortran Compiler: Das Linken von Bibliotheken schlägt fehl

Dies kann vorkommen, wenn gegen Systembibliotheken gelinkt wird (z.B. libX11, libpthread,...). Dafür kann es verschiedene Gründe geben:

  • Überprüfen Sie, ob alle benötigten Bibliotheken angeben wurden.
  • 32 Bit Objekte können nicht mit 64 bit ausführbare Dateien verlinkt werden.
  • Statt -static kann es helfen, den Schalter -i-static zu verwenden. In diesem Fall werden nur die Intel Bibliotheken statisch verlinkt.
 

-- HolgerAngenent - 2010-08-16 \ No newline at end of file

Revision 12010-08-16 - HolgerAngenent

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META TOPICPARENT name="PALMA:english"

-- HolgerAngenent - 2010-08-16

 
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