[MITgcm-support] Compilation with pgi fortran
Zhi-Ping Mei
zhiping_mei at yahoo.com
Fri Jun 20 09:06:43 EDT 2008
Hi Gus,
Thanks for the detailed explanations.
I use Emacs to edit all the files on Linux system. I checked the quote were paired. So we can exclude this possibility.
I am using pgf77 version 6.1.
In the data file, the name list are in the format:
name=value,
But I also have a comma in the last item of each group. I removed the comma from the last item of each group and run the model. I observed the same error.
Below is the text copied from DATA file (for the clarity purposes, I removed some commented lines, but they are shown in the output):
#
# ******************************
# Model parameters
# Continuous equation parameters
# ******************************
&PARM01
tRef= 24.0, 23.0, 22.0, 21.0, 20.0, 19.0,
18.0, 17.0, 16.0, 15.0, 14.0, 13.0,
12.0, 11.0, 10.0, 9.0, 8.0, 7.0,
6.0, 5.0, 4.0, 3.0, 2.0,
sRef= 34.65, 34.75, 34.82, 34.87, 34.90,
34.90, 34.86, 34.78, 34.69, 34.60,
34.58, 34.62, 34.68, 34.72, 34.73,
34.74, 34.73, 34.73, 34.72, 34.72,
34.71, 34.70, 34.69,
no_slip_sides=.false.,
no_slip_bottom=.TRUE.,
viscAz=1.E-3,
viscAh=1.E4,
diffKhT=1.E2,
diffKzT=1.E-5,
diffKhS=1.E2,
diffKzS=1.E-5,
beta=1.E-11,
tAlpha=2.E-4,
sBeta =7.4E-4,
gravity=9.81,
gBaro=9.81,
rigidLid=.FALSE.,
implicitFreeSurface=.true.,
eosType='POLY3',
saltStepping=.TRUE.,
tempStepping=.TRUE.,
momStepping=.TRUE.,
implicitDiffusion=.true.,
implicitViscosity=.true.,
allowFreezing=.false.,
useSingleCpuIO=.TRUE.,
useCDscheme=.FALSE.,
tempAdvScheme = 3,
saltAdvScheme = 3,
/
# **************************
# Elliptic solver parameters
# **************************
&PARM02
cg2dMaxIters=300,
cg2dTargetResidual=1.E-7,
/
# ************************
# Time stepping parameters
# ************************
&PARM03
nIter0=0,
nTimeSteps=35040,
deltaTmom=900.,
deltaTtracer=900.,
deltaTClock=900.,
abEps=0.1,
pChkptFreq = 31104000.,
chkptFreq = 31104000.,
dumpFreq = 604800.,
taveFreq = 604800.,
monitorFreq = 604800.,
tauThetaClimRelax=0.,
tauSaltClimRelax=0.,
periodicExternalForcing=.TRUE.,
externForcingPeriod=2592000.,
externForcingCycle=31104000.,
/
# *******************
# Gridding parameters
# *******************
&PARM04
usingCartesianGrid=.FALSE.,
usingSphericalPolarGrid=.TRUE.,
delX=360*1.E0,
delY=160*1.E0,
delZ=10., 10., 15., 20., 20., 25., 35., 50., 75.,
100., 150., 200., 275., 350., 415., 450., 500.,
500., 500., 500., 500., 500., 500.,
phimin=-80.,
thetamin=0.,
/
# **********
# Data Files
# **********
&PARM05
bathyFile= 'input/bathy_fl.bin',
#hydrogThetaFile= 'input/LEVITUS_1x1_ptmp_NEW_corK',
#hydrogSaltFile= 'input/LEVITUS_1x1_salt_NEW_corK',
zonalWindFile= '',
meridWindFile= '',
thetaClimFile= '',
saltClimFile= '',
surfQFile= '',
EmPmRFile= '',
/
%%%% end of data file
Following are the error message from PBS system of the cluster:
PGFIO-F-228/namelist read/unit=11/end of file reached without finding group.
File name = /tmp/FTNcaaaaybtaz formatted, sequential access record = 141
In source file ini_parms.f, at line number 3496
PGFIO-F-228/namelist read/unit=11/end of file reached without finding group.
PGFIO-F-228/namelist read/unit=11/end of file reached without finding group.
File name = /tmp/FTNcaaaaizBaz formatted, sequential access record = 141
In source file ini_parms.f, at line number 3496
PGFIO-F-228/namelist read/unit=11/end of file reached without finding group.
File name = /tmp/FTNcaaaaaifaz formatted, sequential access record = 141
In source file ini_parms.f,PGFIO-F-228/namelist read/unit=11/end of file reached without finding group.
%%%%%%%
Finally the output of STDOUT.0000:
(PID.TID 0000.0001)
(PID.TID 0000.0001) // ======================================================
(PID.TID 0000.0001) // MITgcm UV
(PID.TID 0000.0001) // =========
(PID.TID 0000.0001) // ======================================================
(PID.TID 0000.0001) // execution environment starting up...
(PID.TID 0000.0001)
(PID.TID 0000.0001) // MITgcmUV version: checkpoint58b_post
(PID.TID 0000.0001) // Build user: meiz0001
(PID.TID 0000.0001) // Build host: masternode001
(PID.TID 0000.0001) // Build date: Thu Jun 19 21:40:00 ADT 2008
(PID.TID 0000.0001)
(PID.TID 0000.0001) // =======================================================
(PID.TID 0000.0001) // Execution Environment parameter file "eedata"
(PID.TID 0000.0001) // =======================================================
(PID.TID 0000.0001) ># Example "eedata" file
(PID.TID 0000.0001) ># Lines beginning "#" are comments
(PID.TID 0000.0001) ># nTx - No. threads per process in X
(PID.TID 0000.0001) ># nTy - No. threads per process in Y
(PID.TID 0000.0001) > &EEPARMS
(PID.TID 0000.0001) > nTx=1,nTy=1
(PID.TID 0000.0001) > /
(PID.TID 0000.0001) ># Note: Some systems use & as the
(PID.TID 0000.0001) ># namelist terminator. Other systems
(PID.TID 0000.0001) ># use a / character (as shown here).
(PID.TID 0000.0001)
(PID.TID 0000.0001) // =======================================================
(PID.TID 0000.0001) // Computational Grid Specification ( see files "SIZE.h" )
(PID.TID 0000.0001) // ( and "eedata" )
(PID.TID 0000.0001) // =======================================================
(PID.TID 0000.0001) nPx = 8 ; /* No. processes in X */
(PID.TID 0000.0001) nPy = 4 ; /* No. processes in Y */
(PID.TID 0000.0001) nSx = 1 ; /* No. tiles in X per process */
(PID.TID 0000.0001) nSy = 1 ; /* No. tiles in Y per process */
(PID.TID 0000.0001) sNx = 45 ; /* Tile size in X */
(PID.TID 0000.0001) sNy = 40 ; /* Tile size in Y */
(PID.TID 0000.0001) OLx = 4 ; /* Tile overlap distance in X */
(PID.TID 0000.0001) OLy = 4 ; /* Tile overlap distance in Y */
(PID.TID 0000.0001) nTx = 1 ; /* No. threads in X per process */
(PID.TID 0000.0001) nTy = 1 ; /* No. threads in Y per process */
(PID.TID 0000.0001) Nr = 23 ; /* No. levels in the vertical */
(PID.TID 0000.0001) nX = 360 ; /* Total domain size in X ( = nPx*nSx*sNx ) */
(PID.TID 0000.0001) nY = 160 ; /* Total domain size in Y ( = nPy*nSy*sNy ) */
(PID.TID 0000.0001) nTiles = 1 ; /* Total no. tiles per process ( = nSx*nSy ) */
(PID.TID 0000.0001) nProcs = 32 ; /* Total no. processes ( = nPx*nPy ) */
(PID.TID 0000.0001) nThreads = 1 ; /* Total no. threads per process ( = nTx*nTy ) */
(PID.TID 0000.0001) usingMPI = F ; /* Flag used to control whether MPI is in use */
(PID.TID 0000.0001) /* note: To execute a program with MPI calls */
(PID.TID 0000.0001) /* it must be launched appropriately e.g */
(PID.TID 0000.0001) /* "mpirun -np 64 ......" */
(PID.TID 0000.0001) useCoupler= F ; /* Flag used to control communications with */
(PID.TID 0000.0001) /* other model components, through a coupler */
(PID.TID 0000.0001)
(PID.TID 0000.0001) ======= Starting MPI parallel Run =========
(PID.TID 0000.0001) My Processor Name = node075
(PID.TID 0000.0001) Located at ( 0, 0) on processor grid (0: 7,0: 3)
(PID.TID 0000.0001) Origin at ( 1, 1) on global grid (1: 360,1: 160)
(PID.TID 0000.0001) North neighbor = processor 0001
(PID.TID 0000.0001) South neighbor = processor 0003
(PID.TID 0000.0001) East neighbor = processor 0004
(PID.TID 0000.0001) West neighbor = processor 0028
(PID.TID 0000.0001) // ======================================================
(PID.TID 0000.0001) // Mapping of tiles to threads
(PID.TID 0000.0001) // ======================================================
(PID.TID 0000.0001) // -o- Thread 1, tiles ( 1: 1, 1: 1)
(PID.TID 0000.0001)
(PID.TID 0000.0001) // ======================================================
(PID.TID 0000.0001) // Tile <-> Tile connectvity table
(PID.TID 0000.0001) // ======================================================
(PID.TID 0000.0001) // Tile number: 000001 (process no. = 000000)
(PID.TID 0000.0001) // WEST: Tile = 000008, Process = 000028, Comm = messages
(PID.TID 0000.0001) // bi = 000001, bj = 000001
(PID.TID 0000.0001) // EAST: Tile = 000002, Process = 000004, Comm = messages
(PID.TID 0000.0001) // bi = 000001, bj = 000001
(PID.TID 0000.0001) // SOUTH: Tile = 000025, Process = 000003, Comm = messages
(PID.TID 0000.0001) // bi = 000001, bj = 000001
(PID.TID 0000.0001) // NORTH: Tile = 000009, Process = 000001, Comm = messages
(PID.TID 0000.0001) // bi = 000001, bj = 000001
(PID.TID 0000.0001)
(PID.TID 0000.0001) // =======================================================
(PID.TID 0000.0001) // Model parameter file "data"
(PID.TID 0000.0001) // =======================================================
(PID.TID 0000.0001) >#
(PID.TID 0000.0001) ># ******************************
(PID.TID 0000.0001) ># Model parameters
(PID.TID 0000.0001) ># Continuous equation parameters
(PID.TID 0000.0001) ># ******************************
(PID.TID 0000.0001) >&PARM01
(PID.TID 0000.0001) >tRef= 24.0,
(PID.TID 0000.0001) > 23.0,
(PID.TID 0000.0001) > 22.0,
(PID.TID 0000.0001) > 21.0,
(PID.TID 0000.0001) > 20.0,
(PID.TID 0000.0001) > 19.0,
(PID.TID 0000.0001) > 18.0,
(PID.TID 0000.0001) > 17.0,
(PID.TID 0000.0001) > 16.0,
(PID.TID 0000.0001) > 15.0,
(PID.TID 0000.0001) > 14.0,
(PID.TID 0000.0001) > 13.0,
(PID.TID 0000.0001) > 12.0,
(PID.TID 0000.0001) > 11.0,
(PID.TID 0000.0001) > 10.0,
(PID.TID 0000.0001) > 9.0,
(PID.TID 0000.0001) > 8.0,
(PID.TID 0000.0001) > 7.0,
(PID.TID 0000.0001) > 6.0,
(PID.TID 0000.0001) > 5.0,
(PID.TID 0000.0001) > 4.0,
(PID.TID 0000.0001) > 3.0,
(PID.TID 0000.0001) > 2.0,
(PID.TID 0000.0001) >sRef= 34.65,
(PID.TID 0000.0001) > 34.75,
(PID.TID 0000.0001) > 34.82,
(PID.TID 0000.0001) > 34.87,
(PID.TID 0000.0001) > 34.90,
(PID.TID 0000.0001) > 34.90,
(PID.TID 0000.0001) > 34.86,
(PID.TID 0000.0001) > 34.78,
(PID.TID 0000.0001) > 34.69,
(PID.TID 0000.0001) > 34.60,
(PID.TID 0000.0001) > 34.58,
(PID.TID 0000.0001) > 34.62,
(PID.TID 0000.0001) > 34.68,
(PID.TID 0000.0001) > 34.72,
(PID.TID 0000.0001) > 34.73,
(PID.TID 0000.0001) > 34.74,
(PID.TID 0000.0001) > 34.73,
(PID.TID 0000.0001) > 34.73,
(PID.TID 0000.0001) > 34.72,
(PID.TID 0000.0001) > 34.72,
(PID.TID 0000.0001) > 34.71,
(PID.TID 0000.0001) > 34.70,
(PID.TID 0000.0001) > 34.69,
(PID.TID 0000.0001) >no_slip_sides=.false.,
(PID.TID 0000.0001) >no_slip_bottom=.TRUE.,
(PID.TID 0000.0001) >viscAz=1.E-3,
(PID.TID 0000.0001) >viscAh=1.E4,
(PID.TID 0000.0001) >diffKhT=1.E2,
(PID.TID 0000.0001) >diffKzT=1.E-5,
(PID.TID 0000.0001) >diffKhS=1.E2,
(PID.TID 0000.0001) >diffKzS=1.E-5,
(PID.TID 0000.0001) >beta=1.E-11,
(PID.TID 0000.0001) >tAlpha=2.E-4,
(PID.TID 0000.0001) >sBeta =7.4E-4,
(PID.TID 0000.0001) >gravity=9.81,
(PID.TID 0000.0001) >gBaro=9.81,
(PID.TID 0000.0001) >rigidLid=.FALSE.,
(PID.TID 0000.0001) >implicitFreeSurface=.true.,
(PID.TID 0000.0001) >eosType='POLY3',
(PID.TID 0000.0001) >saltStepping=.TRUE.,
(PID.TID 0000.0001) >tempStepping=.TRUE.,
(PID.TID 0000.0001) >momStepping=.TRUE.,
(PID.TID 0000.0001) >implicitDiffusion=.true.,
(PID.TID 0000.0001) >implicitViscosity=.true.,
(PID.TID 0000.0001) >allowFreezing=.false.,
(PID.TID 0000.0001) >useSingleCpuIO=.TRUE.,
(PID.TID 0000.0001) >useCDscheme=.FALSE.,
(PID.TID 0000.0001) >tempAdvScheme = 3,
(PID.TID 0000.0001) >saltAdvScheme = 3,
(PID.TID 0000.0001) >/
(PID.TID 0000.0001) >
(PID.TID 0000.0001) ># **************************
(PID.TID 0000.0001) ># Elliptic solver parameters
(PID.TID 0000.0001) ># **************************
(PID.TID 0000.0001) >&PARM02
(PID.TID 0000.0001) >cg2dMaxIters=300,
(PID.TID 0000.0001) >cg2dTargetResidual=1.E-7,
(PID.TID 0000.0001) >/
(PID.TID 0000.0001) >
(PID.TID 0000.0001) ># ************************
(PID.TID 0000.0001) ># Time stepping parameters
(PID.TID 0000.0001) ># ************************
(PID.TID 0000.0001) >&PARM03
(PID.TID 0000.0001) >nIter0=0,
(PID.TID 0000.0001) >nTimeSteps=35040,
(PID.TID 0000.0001) >#Mei deltaTmom=10800.,
(PID.TID 0000.0001) >#Mei
(PID.TID 0000.0001) >deltaTmom=900.,
(PID.TID 0000.0001) >#Mei deltaTtracer=10800.,
(PID.TID 0000.0001) >#Mei
(PID.TID 0000.0001) >deltaTtracer=900.,
(PID.TID 0000.0001) >#Mei deltaTClock =10800.,
(PID.TID 0000.0001) >#Mei
(PID.TID 0000.0001) >deltaTClock=900.,
(PID.TID 0000.0001) >abEps=0.1,
(PID.TID 0000.0001) >pChkptFreq = 31104000.,
(PID.TID 0000.0001) >chkptFreq = 31104000.,
(PID.TID 0000.0001) >#pChkptFreq = 2592000.,
(PID.TID 0000.0001) >#chkptFreq = 2592000.,
(PID.TID 0000.0001) >#Mei dumpFreq = 31104000.,
(PID.TID 0000.0001) >#Mei
(PID.TID 0000.0001) >dumpFreq = 604800.,
(PID.TID 0000.0001) >#Mei taveFreq = 31104000.,
(PID.TID 0000.0001) >#Mei
(PID.TID 0000.0001) >taveFreq = 604800.,
(PID.TID 0000.0001) >#taveFreq = 86400.,
(PID.TID 0000.0001) >#monitorFreq = 10800.,
(PID.TID 0000.0001) >#Mei monitorFreq = 31104000.,
(PID.TID 0000.0001) >#Mei
(PID.TID 0000.0001) >monitorFreq = 604800.,
(PID.TID 0000.0001) >tauThetaClimRelax=0.,
(PID.TID 0000.0001) >tauSaltClimRelax=0.,
(PID.TID 0000.0001) >periodicExternalForcing=.TRUE.,
(PID.TID 0000.0001) >externForcingPeriod=2592000.,
(PID.TID 0000.0001) >externForcingCycle=31104000.,
(PID.TID 0000.0001) >/
(PID.TID 0000.0001) >
(PID.TID 0000.0001) ># *******************
(PID.TID 0000.0001) ># Gridding parameters
(PID.TID 0000.0001) ># *******************
(PID.TID 0000.0001) >&PARM04
(PID.TID 0000.0001) >usingCartesianGrid=.FALSE.,
(PID.TID 0000.0001) >usingSphericalPolarGrid=.TRUE.,
(PID.TID 0000.0001) >delX=360*1.E0,
(PID.TID 0000.0001) >delY=160*1.E0,
(PID.TID 0000.0001) >delZ=10.,
(PID.TID 0000.0001) > 10.,
(PID.TID 0000.0001) > 15.,
(PID.TID 0000.0001) > 20.,
(PID.TID 0000.0001) > 20.,
(PID.TID 0000.0001) > 25.,
(PID.TID 0000.0001) > 35.,
(PID.TID 0000.0001) > 50.,
(PID.TID 0000.0001) > 75.,
(PID.TID 0000.0001) > 100.,
(PID.TID 0000.0001) > 150.,
(PID.TID 0000.0001) > 200.,
(PID.TID 0000.0001) > 275.,
(PID.TID 0000.0001) > 350.,
(PID.TID 0000.0001) > 415.,
(PID.TID 0000.0001) > 450.,
(PID.TID 0000.0001) > 500.,
(PID.TID 0000.0001) > 500.,
(PID.TID 0000.0001) > 500.,
(PID.TID 0000.0001) > 500.,
(PID.TID 0000.0001) > 500.,
(PID.TID 0000.0001) > 500.,
(PID.TID 0000.0001) > 500.,
(PID.TID 0000.0001) >phimin=-80.,
(PID.TID 0000.0001) >thetamin=0.,
(PID.TID 0000.0001) >/
(PID.TID 0000.0001) >
(PID.TID 0000.0001) ># **********
(PID.TID 0000.0001) ># Data Files
(PID.TID 0000.0001) ># **********
(PID.TID 0000.0001) >&PARM05
(PID.TID 0000.0001) >bathyFile= 'input/bathy_fl.bin',
(PID.TID 0000.0001) >#hydrogThetaFile= 'input/LEVITUS_1x1_ptmp_NEW_corK',
(PID.TID 0000.0001) >#hydrogSaltFile= 'input/LEVITUS_1x1_salt_NEW_corK',
(PID.TID 0000.0001) >zonalWindFile= '',
(PID.TID 0000.0001) >meridWindFile= '',
(PID.TID 0000.0001) >thetaClimFile= '',
(PID.TID 0000.0001) >saltClimFile= '',
(PID.TID 0000.0001) >surfQFile= '',
(PID.TID 0000.0001) >EmPmRFile= '',
(PID.TID 0000.0001) >/
(PID.TID 0000.0001)
(PID.TID 0000.0001) S/R INI_PARMS ; starts to read PARM01
%%%%%%%%%%% End of the output.
One more thing, I use pgf77, not pgf90. Does it matter?
In the eesupp/src/nml_set_terminator.F, I see the following lines:
#include "CPP_OPTIONS.h"
#define FTN_NML_F90
#ifndef NML_TERMINATOR
#define NML_TERMINATOR ' &'
#else
#define NML_TERMINATOR ' /'
#endif
What do they do? Are they in conflict with -DNML_TERMINATOR="/" in the build_option file?
Please let me know if you need further information.
Zhi-Ping
--- On Thu, 6/19/08, Gus Correa <gus at ldeo.columbia.edu> wrote:
> From: Gus Correa <gus at ldeo.columbia.edu>
> Subject: Re: [MITgcm-support] Compilation with pgi fortran
> To: "MITgcm Support" <mitgcm-support at mitgcm.org>
> Date: Thursday, June 19, 2008, 10:40 PM
> Hi Zhi-Ping and list
>
> The "official" Fortran90 namelist terminator is
> the slash ("/"),
> but somehow all namelists in the MITgcm example seem to use
> the
> ampersand ("&") as a terminator (see data,
> eedata, and other
> input parameter files).
>
> Some compilers are lax and take the ampersand also.
> PGI was not tolerant, and required the slash as a namelist
> terminator.
> I haven't used the latest PGI versions, so things may
> have changed.
>
> So depending on the compiler, you have to replace the
> namelist terminator
> by using the pre-processor directive
> -DNML_TERMINATOR="/".
> This will strip off the ampersand and replace it by slash
> on all namelists
> on the fly when the program runs.
>
> Indeed, as you noticed, I have a blank before the slash.
> I don't really remember why, but since it is being
> overwritten on the
> namelist file, the blank is probably there for safety, to
> avoid
> concatenating
> the slash with the last value on the namelist.
> So, the blank shouldn't hurt.
>
> Anyway, did you make sure that all the single quotes and
> double quotes
> in the
> pre-processor directives are matched and paired?
> The fact that your netcdf library didn't link,
> after you changed the build_options file,
> suggests to me that maybe the compilation
> got lost on quotes that were not paired.
>
> Another thing to check is if all the namelist items are of
> the form
> name=value,
> and that there is comma at the end (except the last item on
> each namelist).
>
> A more remote possibility, is if you edited your namelist
> files in a Windows
> computer (or an old Mac, or a DOS machine),
> and you if are running the experiment on a Linux machine.
> The line terminators in those computers are different than
> Linux,
> Parsing input files this way is a total mess.
> A couple of computer users here had this problem,
> and it was hard to understand what was going on,
> until they told me where they had been preparing their
> input files.
>
> If this is the case, you should edit your files (data, etc)
> in the Linux
> machine,
> or use a line terminator converter.
> See this article:
>
> http://en.wikipedia.org/wiki/Newline
>
> Otherwise, please send more details on the error messages.
>
> HIH
> Gus Correa
>
> Zhi-Ping Mei wrote:
>
> >Thanks Gus,
> >
> >
> >
> >
> >
> >>Do you have this line on your build_options file,
> >>to define "/" as the namelist terminator?
> >>
> >>DEFINES='-DWORDLENGTH=4
> -DNML_TERMINATOR=" /" '
> >>/" '
> >>
> >>
> >>
> >I have -DWORDLENGTH=4, but did not have
> -DNML_TERMINATOR=" /" '. So I added
> -DNML_TERMINATOR=" /" ' to the DEFINES. I see
> the same problem.
> >
> >Do you mean there is a space before /? I tried that
> either. When a space is put before /, netcdf library
> can't be linked.
> >
> >
> >Zhi-Ping
> >
> >
> >>Zhi-Ping Mei wrote:
> >>
> >>
> >>
> >>>Hell all,
> >>>
> >>>I am trying to compile MITgcm with PGI fortran.
> The
> >>>
> >>>
> >>compilation went fine and the binary mitgcmuv is
> generated.
> >>
> >>
> >>>However, when I run the binary, I got following
> error:
> >>>
> >>>PGFIO-F-228/namelist read/unit=11/end of file
> reached
> >>>
> >>>
> >>without finding group.
> >>
> >>
> >>>File name = /tmp/FTNcaaaaaDxah formatted,
> >>>
> >>>
> >>sequential access record = 85
> >>
> >>
> >>>In source file ini_parms.f,PGFIO-F-228/namelist
> >>>
> >>>
> >>read/unit=11/end of file reached without finding
> group.
> >>
> >>
> >>>PGFIO-F-228/namelist read/unit=11/end of file
> reached
> >>>
> >>>
> >>without finding group.
> >>
> >>
> >>>PGFIO-F-228/namelist read/unit=11/end of file
> reached
> >>>
> >>>
> >>without finding group.
> >>
> >>
> >>>at line number 3496
> >>>...
> >>>
> >>>which appears to be related to reading
> 'data'
> >>>
> >>>When I compiled with g77, I never encountered
> such
> >>>
> >>>
> >>problem. So I suspect it's related to
> compilation.
> >>
> >>
> >>>The following is the lines of build options:
> >>>===================================
> >>>#!/bin/bash
> >>>#
> >>># $Header:
> >>>
> >>>
> >>/u/gcmpack/MITgcm/tools/build_options/linux_ia32_pgf77+mpi,v
> >>1.5 2004/09/25 00:42:14 heimbach Exp $
> >>
> >>
> >>>#
> >>>
> >>>FC='mpif77'
> >>>CC='mpicc'
> >>>LINK='mpif77'
> >>>DEFINES='-DALLOW_USE_MPI -DALWAYS_USE_MPI
> >>>
> >>>
> >>-DWORDLENGTH=4'
> >>
> >>
> >>>CPP='cpp -traditional -P'
> >>>INCLUDES='-I/usr/local/mpich/1.2.5/ip/up/pgi/ssh/include
> >>>
> >>>
> >>-I/usr/local/netcdf/pgi/include'
> >>
> >>
> >>>LIBS='-L/usr/local/mpich/1.2.5/ip/up/pgi/ssh/lib
> >>>
> >>>
> >>-lfmpich -lmpich -L/usr/local/netcdf/pgi/lib'
> >>
> >>
> >>>if test "x$IEEE" = x ; then
> >>> # No need for IEEE-754
> >>> FFLAGS='-byteswapio -r8 -Mnodclchk
> >>>
> >>>
> >>-Mextend'
> >>
> >>
> >>> FOPTIM='-fastsse
> >>>
> >>>
> >>-Mvect=cachesize:524288,transform'
> >>
> >>
> >>>else
> >>> # Try to follow IEEE-754
> >>> FFLAGS='-byteswapio -r8 -Mnodclchk
> >>>
> >>>
> >>-Mextend'
> >>
> >>
> >>> FOPTIM='-O0 -Mvect=sse -Mscalarsse
> >>>
> >>>
> >>-Mcache_align -Mnoflushz -Kieee'
> >>
> >>
> >>>fi
> >>>
> >>>==================================================
> >>>
> >>>and the following are the lines of job
> submission
> >>>
> >>>
> >>script:
> >>
> >>
> >>>``````````````````````````````````````````````````````````````````````````````````````````
> >>>#PBS -S /bin/bash
> >>>#PBS -N mitgcmuv
> >>>#PBS -l nodes=16:ppn=2
> >>>#PBS -l walltime=120:00:00
> >>>#PBS -o qsub.output
> >>>#PBS -j oe
> >>>
> >>># torch.mpi Last Modified Jan 16, 2008,
> Kristian
> >>>
> >>>
> >>Strickland
> >>
> >>
> >>># Determine number of processors
> >>>NPROCS=`wc -l < $PBS_NODEFILE`
> >>>
> >>># Pad the log with extra info
> >>>echo "PBS: qsub was run on
> $PBS_O_HOST"
> >>>echo "PBS: job
> \"$PBS_JOBNAME\"
> >>>
> >>>
> >>submitted while in: $PBS_O_WORKDIR"
> >>
> >>
> >>>echo "PBS: submitted to queue:
> $PBS_O_QUEUE,
> >>>
> >>>
> >>execution in queue: $PBS_QUEUE"
> >>
> >>
> >>>echo "PBS: execution mode is
> >>>
> >>>
> >>$PBS_ENVIRONMENT"
> >>
> >>
> >>>echo "PBS: this job has allocated $NPROCS
> >>>
> >>>
> >>CPUs"
> >>
> >>
> >>>## Next two lines for debugging
> >>>#echo "PBS: node file is $PBS_NODEFILE and
> >>>
> >>>
> >>contains one CPU per node listed:"
> >>
> >>
> >>>#echo `cat $PBS_NODEFILE`
> >>>echo "PBS: PATH = $PBS_O_PATH"
> >>>echo ----------------------------------------
> >>>
> >>>export
> >>>
> >>>
> >>MPICH="/usr/local/mpich/1.2.5/ip/up/pgi/ssh"
> >>
> >>
> >>>export MPICH_PATH="${MPICH}/bin"
> >>>export MPICH_LIB="${MPICH}/lib"
> >>>export PATH="${MPICH_PATH}:${PATH}"
> >>>export
> >>>
> >>>
> >>LD_LIBRARY_PATH="${MPICH_LIB}:${LD_LIBRARY_PATH}"
> >>
> >>
> >>>cd $PBS_O_WORKDIR
> >>>
> >>># Run the parallel MPI executable
> "a.out"
> >>>mpirun -machinefile ${PBS_NODEFILE} -np $NPROCS
>
> >>>
> >>>
> >>./${PBS_JOBNAME}
> >>
> >>
> >>>#>& out.dat
> >>>```````````````````````````````````````````````````````````````````
> >>>
> >>>I appreciate someone who are familiar with
> compilation
> >>>
> >>>
> >>take a look and give me some advices. Thanks in
> advance,
> >>
> >>
> >>>Zhi-Ping
> >>>
> >>>Mount Allison University
> >>>New Brunswick
> >>>Canda
> >>>
> >>>
> >>>
> >>>_______________________________________________
> >>>MITgcm-support mailing list
> >>>MITgcm-support at mitgcm.org
> >>>http://mitgcm.org/mailman/listinfo/mitgcm-support
> >>>
> >>>
> >>>
> >>>
> >>_______________________________________________
> >>MITgcm-support mailing list
> >>MITgcm-support at mitgcm.org
> >>http://mitgcm.org/mailman/listinfo/mitgcm-support
> >>
> >>
> >
> >
> >
> >_______________________________________________
> >MITgcm-support mailing list
> >MITgcm-support at mitgcm.org
> >http://mitgcm.org/mailman/listinfo/mitgcm-support
> >
> >
>
> _______________________________________________
> MITgcm-support mailing list
> MITgcm-support at mitgcm.org
> http://mitgcm.org/mailman/listinfo/mitgcm-support
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