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PGI 6.1, GAMESS, Opteron, and Suse10

 
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willsd



Joined: 03 Jan 2006
Posts: 5

PostPosted: Thu Jan 26, 2006 7:06 am    Post subject: PGI 6.1, GAMESS, Opteron, and Suse10 Reply with quote

I recently installed PGI workstation 6.1 and followed the directions on the PGI GAMESS page for tuning the GAMESS compile scripts for PGI 6.0 and amd-64. I copyed the PGI BLAS library to where the GAMESS lked script wanted it and compile completed. I ended up with the two exectuables ddikick.x and gamess.00.x that I was supposed to have.

BUT I got lost of errors with the runall test so just focused on exam01. The job gets to printing moments of inertia then dies with a segmentation fault. Output is below:

willsd@freesun:/usr/local/apps/gamess/gamess> ./rungms exam01
> >>----- GAMESS execution script -----
> >>This job is running on host freesun
> >>under operating system Linux at Wed Jan 25 08:06:37 EST 2006
> >>Available scratch disk space (Kbyte units) at beginning of the job is
> >>Filesystem 1K-blocks Used Available Use% Mounted on
> >>/dev/sda3 243080064 11847420 231232644 5% /
> >>cp exam01.inp /usr/local/apps/gamess/gamess/willsd/exam01.F05
> >>unset echo
> >>setenv ERICFMT /usr/local/apps/gamess/gamess/ericfmt.dat
> >>setenv EXTBAS /dev/null
> >>setenv IRCDATA /usr/local/apps/gamess/gamess/scr/exam01.irc
> >>
> >>SNIP
> >>
> >>
> >>
> >>Distributed Data Interface kickoff program.
> >>Initiating 1 compute processes on 1 nodes to run the following command:
> >>/usr/local/apps/gamess/gamess/gamess.00.x exam01
> >>
> >> ******************************************************
> >> * GAMESS VERSION = 22 NOV 2004 (R1) *
> >> * FROM IOWA STATE UNIVERSITY *
> >> * M.W.SCHMIDT, K.K.BALDRIDGE, J.A.BOATZ, S.T.ELBERT, *
> >> * M.S.GORDON, J.H.JENSEN, S.KOSEKI, N.MATSUNAGA, *
> >> * K.A.NGUYEN, S.J.SU, T.L.WINDUS, *
> >> * TOGETHER WITH M.DUPUIS, J.A.MONTGOMERY *
> >> * J.COMPUT.CHEM. 14, 1347-1363(1993) *
> >> ***************** AMD 64 BIT VERSION *****************
> >>
> >> SINCE 1993, STUDENTS AND POSTDOCS WORKING AT IOWA STATE UNIVERSITY
> >> AND ALSO IN THEIR VARIOUS JOBS AFTER LEAVING ISU HAVE MADE IMPORTANT
> >> CONTRIBUTIONS TO THE CODE:
> >> IVANA ADAMOVIC, CHRISTINE AIKENS, ROB BELL, PRADIPTA BANDYOPADHYAY,
> >> BRETT BODE, GALINA CHABAN, WEI CHEN, CHEOL HO CHOI, PAUL DAY,
> >> TIM DUDLEY, DMITRI FEDOROV, GRAHAM FLETCHER, MARK FREITAG,
> >> KURT GLAESEMANN, GRANT MERRILL, HEATHER NETZLOFF, RYAN OLSON,
> >> MIKE PAK, JIM SHOEMAKER, TETSUYA TAKETSUGU, SIMON WEBB.
> >>
> >> ADDITIONAL CODE HAS BEEN PROVIDED BY COLLABORATORS IN OTHER GROUPS:
> >> IOWA STATE UNIVERSITY: JOE IVANIC, KLAUS RUEDENBERG
> >> UNIVERSITY OF TOKYO: KIMIHIKO HIRAO, HARUYUKI NAKANO, TAKAHITO
> >> NAKAJIMA, TAKAO TSUNEDA, MUNEAKI KAMIYA, SUSUMU YANAGISAWA,
> >> KIYOSHI YAGI
> >> ODENSE UNIVERSITY: FRANK JENSEN
> >> UNIVERSITY OF IOWA: VISVALDAS KAIRYS, HUI LI
> >> NATIONAL INST. OF STANDARDS AND TECHNOLOGY: WALT STEVENS, DAVID GARMER
> >> UNIVERSITY OF PISA: BENEDETTA MENNUCCI, JACOPO TOMASI
> >> UNIVERSITY OF MEMPHIS: HENRY KURTZ, PRAKASHAN KORAMBATH
> >> UNIVERSITY OF ALBERTA: MARIUSZ KLOBUKOWSKI
> >> UNIVERSITY OF NEW ENGLAND: MARK SPACKMAN
> >> MIE UNIVERSITY: HIROAKI UMEDA
> >> MICHIGAN STATE UNIVERSITY: KAROL KOWALSKI, PIOTR PIECUCH
> >> UNIVERSITY OF SILESIA: MONIKA MUSIAL, STANISLAW KUCHARSKI
> >> FACULTES UNIVERSITAIRES NOTRE-DAME DE LA PAIX:
> >> OLIVIER QUINET, BENOIT CHAMPAGNE
> >> UNIVERSITY OF CALIFORNIA - SANTA BARBARA: BERNARD KIRTMAN
> >> INSTITUTE FOR MOLECULAR SCIENCE: KAZUYA ISHIMURA AND SHIGERU NAGASE
> >>
> >>EXECUTION OF GAMESS BEGUN Wed Jan 25 08:06:38 2006
> >>
> >> ECHO OF THE FIRST FEW INPUT CARDS -
> >>INPUT CARD>! EXAM01.
> >>INPUT CARD>! 1-A-1 CH2 RHF geometry optimization using GAMESS.
> >>INPUT CARD>!
> >>INPUT CARD>! Although internal coordinates are used (COORD=ZMAT),
> >>INPUT CARD>! the optimization is done in Cartesian space (NZVAR=0).
> >>INPUT CARD>! This run uses a criterion (OPTTOL) on the gradient
> >>INPUT CARD>! which is tighter than is normally used.
> >>INPUT CARD>!
> >>INPUT CARD>! This job tests the sp integral module, the RHF module,
> >>INPUT CARD>! and the geometry optimization module.
> >>INPUT CARD>!
> >>INPUT CARD>! Using the default search METHOD=STANDARD,
> >>INPUT CARD>! FINAL E= -37.2322678015, 8 iters, RMS grad= .0264308
> >>INPUT CARD>! FINAL E= -37.2308175306, 7 iters, RMS grad= .0320881
> >>INPUT CARD>! FINAL E= -37.2375723427, 7 iters, RMS grad= .0056557
> >>INPUT CARD>! FINAL E= -37.2379944433, 6 iters, RMS grad= .0017901
> >>INPUT CARD>! FINAL E= -37.2380387836, 8 iters, RMS grad= .0003391
> >>INPUT CARD>! FINAL E= -37.2380397697, 6 iters, RMS grad= .0000030
> >>INPUT CARD>!
> >>INPUT CARD> $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE COORD=ZMT NZVAR=0 $END
> >>INPUT CARD> $SYSTEM TIMLIM=2 MEMORY=100000 $END
> >>INPUT CARD> $STATPT OPTTOL=1.0E-5 $END
> >>INPUT CARD> $BASIS GBASIS=STO NGAUSS=2 $END
> >>INPUT CARD> $GUESS GUESS=HUCKEL $END
> >>INPUT CARD> $DATA
> >>INPUT CARD>Methylene...1-A-1 state...RHF/STO-2G
> >>INPUT CARD>Cnv 2
> >>INPUT CARD>
> >>INPUT CARD>C
> >>INPUT CARD>H 1 rCH
> >>INPUT CARD>H 1 rCH 2 aHCH
> >>INPUT CARD>
> >>INPUT CARD>rCH=1.09
> >>INPUT CARD>aHCH=110.0
> >>INPUT CARD> $END
> >>
> >>..... DONE SETTING UP THE RUN .....
> >> 100000 WORDS OF MEMORY AVAILABLE
> >>
> >> BASIS OPTIONS
> >> -------------
> >> GBASIS=STO IGAUSS= 2 POLAR=NONE
> >> NDFUNC= 0 NFFUNC= 0 DIFFSP= F
> >> NPFUNC= 0 DIFFS= F
> >>
> >>
> >> RUN TITLE
> >> ---------
> >>Methylene...1-A-1 state...RHF/STO-2G
> >>
> >>THE POINT GROUP OF THE MOLECULE IS CNV
> >>THE ORDER OF THE PRINCIPAL AXIS IS 2
> >>
> >>YOUR FULLY SUBSTITUTED Z-MATRIX IS
> >>C
> >>H 1 1.0900000
> >>H 1 1.0900000 2 110.0000
> >>
> >>THE MOMENTS OF INERTIA ARE (AMU-ANGSTROM**2)
> >>IXX= 0.675 IYY= 1.607 IZZ= 2.281
> >>DDI Process 0: trapped a segmentation fault (SIGSEGV).
> >>ddikick.x: application process 0 quit unexpectedly.
> >>ddikick.x: Fatal error detected.
> >>The error is most likely to be in the application, so check for
> >>input errors, disk space, memory needs, application bugs, etc.
> >>ddikick.x will now clean up all processes, and exit...
> >>ddikick.x: Sending kill signal to DDI processes.
> >>ddikick.x: Execution terminated due to error(s).
> >>unset echo
> >>----- accounting info -----
> >>Wed Jan 25 08:06:39 EST 2006
> >>Files used on the master node freesun were:
> >>-rw-r--r-- 1 willsd users 1086 2006-01-25 08:06
> >>/usr/local/apps/gamess/gamess/willsd/exam01.F05
> >>-rw-r--r-- 1 willsd users 163680 2006-01-25 08:06
> >>/usr/local/apps/gamess/gamess/willsd/exam01.F10
> >>0.344u 0.108s 0:01.67 26.3% 0+0k 0+0io 0pf+0w
> >>willsd@freesun:/usr/local/apps/gamess/gamess>

Has anyone built a working GAMESS on suse 10 with PGI 6.1 on an opteron box? Is this combination of hardware/software too new to have been tested? Anyone know how to diagnose this error and fix it?

I can supply other information (contents of .bashrc....) if needed...

Thanks,
Steve Williams
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brentl



Joined: 20 Jul 2004
Posts: 132

PostPosted: Thu Jan 26, 2006 4:17 pm    Post subject: Reply with quote

Hi Steve,

Mat did our 6.1 GAMESS testing and he is on the road this week. He will get back to you once he returns.

- Brent
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mkcolg



Joined: 30 Jun 2004
Posts: 6134
Location: The Portland Group Inc.

PostPosted: Thu Jan 26, 2006 9:14 pm    Post subject: Reply with quote

Hi Steve,

As Brent posted, I am out of the office this week but will take a look when I get back next week. I have thoughly tested the 6.1 compiler with Gamess but did not see the problem you reported. Granted, I was using the June 2005 version of Gamess on SuSE 9.3. I'll try again as see what I can find.

- Mat
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mkcolg



Joined: 30 Jun 2004
Posts: 6134
Location: The Portland Group Inc.

PostPosted: Wed Feb 01, 2006 11:04 am    Post subject: Reply with quote

Hi Steve,

I successfully built and ran the November 22, 2004 version of Gamess on a SuSE 10 system using the 6.1 compilers. I followed the directions posted [url=http://www.pgroup.com/resources/gamess/v112204_pgi60_64.htm\]on the "Tips & Techniques" page.[/url] As you noted, you need to change the lked script to have LIBRARIES set to "-lacml" instead of having it in the LDOPTS.

Could you please try again to see if you might have missed something? Also, be sure that you were following the 64-bit guide since using the 32-bit guide with the 64-bit compilers will lead to the segmentation violation you encountered.

Thanks,
Mat
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