Contacted developer of CMAQ

Turns out the guy who wrote the CMAQ build process is in Dr. Sandu's research group. He walked through the process with me and showed me how to circumvent the CVS issue. I'll begin adding print statements to driver.F until I find the call. He suspects the segfalt is occuring in sciproc.F.

Other suggestions:
1) Reduce time to 1hr instead of 24 until we get this working
2) Turn on MPI
3) Change bldit script to pull from local BLD directory instead of MODELS directory

NetCDF from Dr. Sandu

I spoke with Dr. Sandu about the NetCDF compilation troubles. I'm fairly certain our segfault is associated with the NetCDF libraries on ene-411-lmarr. Dr. Sandu gave me a precompiled NetCDF which his group uses frequently on System X. It's in /nfs/home/jlinford/anuragr/Lib/netcdf-3.5.0. I will try linking CMAQ against this library tomorrow.

NetCDF on System X

Tried building NetCDF on SystemX. Chances are good a working NetCDF is installed somewhere, but I have yet to find it.


sysx1:~/lmarr/netcdf/netcdf-3.6.0-p1/src jlinford$ export CC=/usr/bin/cc
sysx1:~/lmarr/netcdf/netcdf-3.6.0-p1/src jlinford$ export FC=xlf
sysx1:~/lmarr/netcdf/netcdf-3.6.0-p1/src jlinford$ export F90xlf90
sysx1:~/lmarr/netcdf/netcdf-3.6.0-p1/src jlinford$ export F90FLAGS="-qsuffix=cpp=f90"
sysx1:~/lmarr/netcdf/netcdf-3.6.0-p1/src jlinford$ export CPPFLAGS="-Df2cFortran -DIBMR2Fortran"
sysx1:~/lmarr/netcdf/netcdf-3.6.0-p1/src jlinford$ ./configure

....

checking "xlf" as Fortran-90 compiler... works

....

sysx1:~/lmarr/netcdf/netcdf-3.6.0-p1/src jlinford$ make

....

Making `all' in directory /nfs/home/jlinford/lmarr/netcdf/netcdf-3.6.0-p1/src/f90

xlf -c -qsuffix=cpp=f90 typeSizes.f90
"typeSizes.f90", line 30.0: 1515-005 (S) Continuation line is not permitted at b eginning of program or after INCLUDE, EJECT, @PROCESS statements or comment directive. Line is ignored.
"typeSizes.f90", line 31.0: 1515-005 (S) Continuation line is not permitted at b eginning of program or after INCLUDE, EJECT, @PROCESS statements or comment directive. Line is ignored.
"typeSizes.f90", line 32.0: 1515-005 (S) Continuation line is not permitted at b eginning of program or after INCLUDE, EJECT, @PROCESS statements or comment directive. Line is ignored.
"typeSizes.f90", line 33.0: 1515-005 (S) Continuation line is not permitted at b eginning of program or after INCLUDE, EJECT, @PROCESS statements or comment directive. Line is ignored.
"typeSizes.f90", line 34.60: 1515-022 (S) Syntax Error: Extra token " , " was found. The token is ignored.
"typeSizes.f90", line 34.62: 1515-018 (S) Incorrect character found in source at line 34 in column 62. Hexadecimal value of character is 26.
"typeSizes.f90", line 35.60: 1515-022 (S) Syntax Error: Extra token " , " was found. The token is ignored.
"typeSizes.f90", line 35.62: 1515-018 (S) Incorrect character found in source at line 35 in column 62. Hexadecimal value of character is 26.
"typeSizes.f90", line 38.7: 1515-022 (S) Syntax Error: Extra token " ger " was found. The token is ignored.
"typeSizes.f90", line 38.10: 1515-022 (S) Syntax Error: Extra token " , " was found. The token is ignored.
"typeSizes.f90", line 38.12: 1515-022 (S) Syntax Error: Extra token " parameter " was found. The token is ignored.
"typeSizes.f90", line 38.22: 1515-022 (S) Syntax Error: Extra token " :: " was found. The token is ignored.
"typeSizes.f90", line 38.66: 1515-018 (S) Incorrect character found in source at line 38 in column 66. Hexadecimal value of character is 26.
"typeSizes.f90", line 39.72: 1515-020 (S) Syntax Error: Token " ) " is missing. A token is supplied.
"typeSizes.f90", line 42.7: 1515-019 (S) Syntax is incorrect.
"typeSizes.f90", line 55.64: 1515-018 (S) Incorrect character found in source at line 55 in column 64. Hexadecimal value of character is 26.
"typeSizes.f90", line 56.24: 1515-019 (S) Syntax is incorrect.
"typeSizes.f90", line 56.64: 1515-018 (S) Incorrect character found in source at line 56 in column 64. Hexadecimal value of character is 26.
"typeSizes.f90", line 57.22: 1515-019 (S) Syntax is incorrect.
"typeSizes.f90", line 57.56: 1515-018 (S) Incorrect character found in source at line 57 in column 56. Hexadecimal value of character is 26.
"typeSizes.f90", line 58.22: 1515-019 (S) Syntax is incorrect.
"typeSizes.f90", line 59.21: 1515-019 (S) Syntax is incorrect.
"typeSizes.f90", line 61.21: 1515-019 (S) Syntax is incorrect.
"typeSizes.f90", line 63.3: 1515-017 (S) Label contains characters that are not permitted. Label is ignored.
"typeSizes.f90", 1515-002 (S) END card is missing. One is assumed.
** _main === End of Compilation 1 ===
1501-511 Compilation failed for file typeSizes.f90.
make[2]: *** [typeSizes.o] Error 1
make[1]: *** [subdir_target] Error 1
make: *** [f90/all] Error 2

Guess it doesn't work out of the box. Why does NetCDF have to be such a royal pain?!? Was really hoping that would just work. Back to ene-411-lmarr tomorrow.....

Began installation on System X

Just to see what would happen, I've copied CMAQ and associated files to System X and started the installation process. System X has IBM's fortran compiler which is (perhaps) slightly better supported than Intel's and GNU's.

Trying to skip NetCDF Installation

Will try to use NetCDF library from Linsey to save time.

NetCDF Installation

Following instructions from CVS_NETCDF.txt in section "Instructions for building netCDF-3.6.0-p1 for LINUX"

Downloaded http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-3.6.0-p1.tar.gz to /home/jlinford/models/jlinford/tgz/

[jlinford@ene-411-lmarr netcdf]$ cd /home/jlinford/models/jlinford/netcdf/
[jlinford@ene-411-lmarr netcdf]$ tar xvzf ../tgz/netcdf-3.6.0-p1.tar.gz
[jlinford@ene-411-lmarr netcdf]$ cd netcdf-3.6.0-p1/src/
[jlinford@ene-411-lmarr src]$ gedit INSTALL &
[jlinford@ene-411-lmarr src]$ export FC="/opt/intel/fc/9.0/bin/ifort"
[jlinford@ene-411-lmarr src]$ export CC=gcc
[jlinford@ene-411-lmarr src]$ export FFLAGS="-02"
[jlinford@ene-411-lmarr src]$ export CPPFLAGS="-DNDEBUG -DpgiFortran -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE"
[jlinford@ene-411-lmarr src]$ ./configure
[jlinford@ene-411-lmarr src]$ make

......

make[2]: Entering directory `/home/jlinford/models/jlinford/netcdf/netcdf-3.6.0-p1/src/fortran'
gcc -c -g -I../libsrc -DNDEBUG -DpgiFortran -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE fort-attio.c
In file included from fort-attio.c:6:
ncfortran.h:27:42: NF_INT_IS_C_... not defined: No such file or directory
fort-attio.c:12: error: syntax error before "NF_INTEGER"
fort-attio.c:12: error: syntax error before '*' token
fort-attio.c:12: error: syntax error before numeric constant

......

[jlinford@ene-411-lmarr src]$ vi fortran/nfconfig.inc
Line 83: #define NF_INT_IS_C_INT 1
[jlinford@ene-411-lmarr src]$ make

......

Not making `f90/all' because no FORTRAN-90 compiler

......

CMAQ Installation

Downloaded the following to /home/jlinford/models/jlinford/tgz

-rw-rw-r-- 1 jlinford jlinford 1475359 Sep 19 09:25 ioapi-3.0.tar.gz
-rw-rw-r-- 1 jlinford jlinford 329984842 Sep 19 09:48 M3DATA.CMAQv4.5.1.tar.gz
-rw-rw-r-- 1 jlinford jlinford 345789596 Sep 19 09:48 M3DATA_REF.CMAQv4.5.1.tar.gz
-rw-rw-r-- 1 jlinford jlinford 22390057 Sep 19 09:25 M3DOCS.CMAQv4.5.1.tar.gz
-rw-rw-r-- 1 jlinford jlinford 5128159 Sep 19 09:24 M3MODELS.CMAQv4.5.1.tar.gz
-rw-rw-r-- 1 jlinford jlinford 302564 Sep 19 09:24 M3SCRIPTS.CMAQv4.5.1.tar.gz
-rw-rw-r-- 1 jlinford jlinford 883888 Sep 19 09:26 netcdf.tar.gz

Copied Linsey's tutorial.env:



[jlinford@ene-411-lmarr cmaq]$ cp /opt/cmaq/cmaq-4.5.1/tutorial.env /home/jlinford/models/jlinford/cmaq

Edited tutorial.env to fit my environment:

[jlinford@ene-411-lmarr cmaq]$ cat tutorial.env
# env.sh--sets environment variables for running CMAQ

export M3HOME=/home/jlinford/models/jlinford/cmaq
export M3MODEL=$M3HOME/models
export M3LIB=$M3HOME/lib
export M3DATA=/mnt/data/shenair/tutorial
export WORK=$M3HOME/scripts

# location of modules
export MODLOC=$M3HOME/scripts/moddir

[jlinford@ene-411-lmarr cmaq]$ source tutorial.env