[GE users] lam tight and host names

Davide Cittaro davide.cittaro at ifom-ieo-campus.it
Wed Feb 28 14:22:49 GMT 2007


Hi
On Feb 28, 2007, at 2:58 PM, Reuti wrote:

> Try changing:
>
>       host=`echo $line|cut -f1 -d" "|cut -f1 -d"."`
>
> to
>
>       host=`echo $line|cut -f1 -d" "`

That definitely works but now I see something strange.

$ qstat -f -ne -g t
queuename                      qtype used/tot. load_avg arch           
states
------------------------------------------------------------------------ 
----
all.q at alpha1.bioinfo.ifom-ieo- BIP   1/1       0.39     lx24-alpha
    3172 1.05500 mbtest2.sh dcittaro     r     02/28/2007 15:16:27 SLAVE
------------------------------------------------------------------------ 
----
all.q at ia32.bioinfo.ifom-ieo-ca BIP   1/2       0.26     lx26-x86
    3172 1.05500 mbtest2.sh dcittaro     r     02/28/2007 15:16:27 SLAVE
------------------------------------------------------------------------ 
----
all.q at node1.xtal.ifom-ieo-camp BIP   1/4       0.28     lx26-x86
    3172 1.05500 mbtest2.sh dcittaro     r     02/28/2007 15:16:27  
MASTER
                                                                   SLAVE
------------------------------------------------------------------------ 
----
all.q at node2.xtal.ifom-ieo-camp BIP   1/4       0.27     lx26-x86
    3172 1.05500 mbtest2.sh dcittaro     r     02/28/2007 15:16:27 SLAVE
------------------------------------------------------------------------ 
----
all.q at node3.sge.ifom-ieo-campu BIP   1/4       0.24     lx26-amd64
    3172 1.05500 mbtest2.sh dcittaro     r     02/28/2007 15:16:27 SLAVE
------------------------------------------------------------------------ 
----
all.q at node3.xtal.ifom-ieo-camp BIP   1/4       0.29     lx26-x86
    3172 1.05500 mbtest2.sh dcittaro     r     02/28/2007 15:16:27 SLAVE
------------------------------------------------------------------------ 
----
all.q at node4.xtal.ifom-ieo-camp BIP   1/4       0.28     lx26-x86
    3172 1.05500 mbtest2.sh dcittaro     r     02/28/2007 15:16:27 SLAVE
------------------------------------------------------------------------ 
----
all.q at node5.sge.ifom-ieo-campu BIP   1/4       0.28     lx26-amd64
    3172 1.05500 mbtest2.sh dcittaro     r     02/28/2007 15:16:27 SLAVE
------------------------------------------------------------------------ 
----
all.q at node5.xtal.ifom-ieo-camp BIP   1/4       0.33     lx26-x86
    3172 1.05500 mbtest2.sh dcittaro     r     02/28/2007 15:16:27 SLAVE
------------------------------------------------------------------------ 
----
all.q at special.xtal.ifom-ieo-ca BIP   1/4       0.27     lx26-x86
    3172 1.05500 mbtest2.sh dcittaro     r     02/28/2007 15:16:27 SLAVE

so everything seems to work, but:

$ rsh node1.xtal.ifom-ieo-campus.it ps -efHwww
[..]

root      5563  5305  0 15:16 ?        00:00:00     sge_shepherd-3172  
-bg
dcittaro  5788  5563  0 15:16 ?        00:00:00       bash /opt/sge/ 
bioinfo/spool/node1/job_scripts/3172
dcittaro  5789  5788  0 15:16 ?        00:00:00         perl /usr/bin/ 
mpiexec /usr/bin/mb-mpi mb_comm.txt
dcittaro  5791  5789  0 15:16 ?        00:00:00           mpirun  
lam_appschema_NVqcI9
dcittaro  5561     1  0 15:14 ?        00:00:00   /usr/bin/lamd -H  
85.239.175.25 -P 50589 -n 1 -o 0 -sessionsuffix sge-3171-undefined
dcittaro  5643     1  0 15:16 ?        00:00:00   /usr/bin/lamd -H  
85.239.175.21 -P 40954 -n 0 -o 0 -sessionsuffix sge-3172-undefined
dcittaro  5792  5643  0 15:16 ?        00:00:00     /usr/bin/mb-mpi  
mb_comm.txt

[..]

but

rsh node5.sge.ifom-ieo-campus.it ps -efHwww
[..]
dcittaro  5981     1  0 15:14 ?        00:00:00   /usr/bin/lamd -H  
85.239.175.25 -P 50589 -n 8 -o 0 -sessionsuffix sge-3171-undefined
dcittaro  5992     1  0 15:16 ?        00:00:00   /usr/bin/lamd -H  
85.239.175.21 -P 40954 -n 8 -o 0 -sessionsuffix sge-3172-undefined

and so on for each SLAVE node. It seems that my process has been  
spawned but not started...

d
/*
Davide Cittaro
HPC and Bioinformatics Systems @ Informatics Core

IFOM - Istituto FIRC di Oncologia Molecolare
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
e-mail: davide.cittaro at ifom-ieo-campus.it
*/





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