[molpro-user] test job hangs on FC2 Xeon Node

Dr Seth OLSEN s.olsen1 at uq.edu.au
Tue Nov 23 06:16:54 GMT 2004


Hello Molpro-Users,

As outlined in previous communiques, I have been having no luck in getting molpro2002.6 to run on a Dual Xeon node with Fedora Core 2, either as the installed rpm or as a self-compiled version done with ifc7 or ifc8.  The problem is as follows.  After the integral sort, the process writes no more to output but becomes unkillable with 99.9%CPU and 1.0%Mem as given by 'top'.

In order to help diagnose the problem, I have turned the 'gprint,io,cpu' directive on in a given failing job (bccd_opt.test).  The following are the last lines written to output for that job with the io printing turned on:

 EXTENDING RECORD    1300.1 BY        34949. WORDS TO      38820. IMPLEMENTATION=df    EXTENSION 0
 
 NUMBER OF SORTED TWO-ELECTRON INTEGRALS:      34949.     BUFFER LENGTH:  32768
 NUMBER OF SEGMENTS:   1  SEGMENT LENGTH:      34949      RECORD LENGTH: 524288
 
 Memory used in sort:       0.59 MW
 OPENW FILE 24  NAME=/scratch/root/eaf_T2400002627.TMP  IMPLEMENTATION=eaf   STATUS=scratch   HANDLE=     2
 OPEN EAF FILE 24  NAME=  IMPLEMENTATION=eaf
 CLOSEW FILE 21  NAME=eaf_T2100002627.TMP  IMPLEMENTATION=eaf   HANDLE=     1
 CLOSE EAF FILE 21

To determine what files might be opened by molpro at the time that the program stops functioning, I issue a 'lsof | grep molpro' command while the program is running in it's 'unkillable' final status.  The following is the output of that command:

bash      2210     root  cwd    DIR        8,1    12288     295282 /opt/molpro/testjobs
molpro    2624     root  cwd    DIR        8,2     4096    2796193 /scratch/root
molpro    2624     root  rtd    DIR        8,1     4096          2 /
molpro    2624     root  txt    REG        8,1    41552     491923 /usr/local/lib/molpro-mpp-Linux-i686-i4-2002.6/molpro
molpro    2624     root  mem    REG        8,1  1455084      82119 /lib/tls/libc-2.3.3.so
molpro    2624     root  mem    REG        8,1   106892     375519 /lib/ld-2.3.3.so
molpro    2624     root    0u   CHR      136,1                   3 /dev/pts/1
molpro    2624     root    1u   CHR      136,1                   3 /dev/pts/1
molpro    2624     root    2u   CHR      136,1                   3 /dev/pts/1
molpro    2624     root    4u   REG        8,1      823      18013 /tmp/tmpfuX2LXr (deleted)
parallel  2626     root  txt    REG        8,1    30180     491926 /usr/local/lib/molpro-mpp-Linux-i686-i4-2002.6/parallel
parallel  2626     root    1u   REG        8,1    12113     295235 /opt/molpro/testjobs/bccd_opt.out
molprop_2 2627     root  cwd    DIR        8,2     4096    2796193 /scratch/root
molprop_2 2627     root  rtd    DIR        8,1     4096          2 /
molprop_2 2627     root  txt    REG        8,1 19346064     491925 /usr/local/lib/molpro-mpp-Linux-i686-i4-2002.6/molprop_2002_6_p4_tcgmsg.exe
molprop_2 2627     root  mem    REG        8,1    96248     375542 /lib/libnsl-2.3.3.so
molprop_2 2627     root  mem    REG        8,1   106892     375519 /lib/ld-2.3.3.so
molprop_2 2627     root  mem    REG        8,1  1455084      82119 /lib/tls/libc-2.3.3.so
molprop_2 2627     root  mem    REG        8,1   214796      82121 /lib/tls/libm-2.3.3.so
molprop_2 2627     root  mem    REG        8,1    43528     375552 /lib/libnss_nis-2.3.3.so
molprop_2 2627     root  mem    REG        8,1    50944     375549 /lib/libnss_files-2.3.3.so
molprop_2 2627     root    0u   REG        8,1      823      18013 /tmp/tmpfuX2LXr (deleted)
molprop_2 2627     root    1u   REG        8,1    12113     295235 /opt/molpro/testjobs/bccd_opt.out
molprop_2 2627     root    2u   CHR      136,1                   3 /dev/pts/1
molprop_2 2627     root    3u  IPv4       4464                 TCP sphinx128.giza:32846->sphinx128.giza:32844 (ESTABLISHED)
molprop_2 2627     root    4u   REG        8,1     1457      18014 /tmp/forttempG1uyhO
molprop_2 2627     root    5u   REG        8,1       74      18015 /tmp/forttempfYdJb0
molprop_2 2627     root    6u   REG        8,1        0      18016 /tmp/forttemp2hFU5b
molprop_2 2627     root    7u   REG        8,1        0      18017 /tmp/forttemp9p96Zn
molprop_2 2627     root    8u   REG        8,2  3006888    2796194 /scratch/root/df_T0100002627.TMP (deleted)
molprop_2 2627     root    9u   REG        8,2   182344    2796195 /scratch/root/df_T0200002627.TMP (deleted)
molprop_2 2627     root   10u   REG        8,2   182344    2796196 /scratch/root/df_T0300002627.TMP (deleted)
molprop_2 2627     root   11u   REG        8,2        0    2796197 /scratch/root/df_T0400002627.TMP (deleted)
molprop_2 2627     root   12r   REG        8,1   476967     491914 /usr/local/lib/molpro-mpp-Linux-i686-i4-2002.6/libmol.index
molprop_2 2627     root   13u   REG        8,2  3428352    2796199 /scratch/root/eaf_T2400002627.TMP (deleted)

So, it appears that the *.TMP files that molpro has most recently opened and closed are listed as deleted but still open.  I cannot find these files in the specified directory, which makes sense if they are deleted, but if they are deleted than how can they be currently open files?

Cheers,

Seth Olsen



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Dr Seth Olsen, PhD
Postdoctoral Fellow, Computational Systems Biology Group
Centre for Computational Molecular Science
Chemistry Building,
The University of Queensland
Qld 4072, Brisbane, Australia

tel (617) 33653732
fax (617) 33654623
email: s.olsen1 at uq.edu.au
Web: www.ccms.uq.edu.au 

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