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compiling problem with WRFV3
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liliknn



Joined: 26 Oct 2008
Posts: 3

PostPosted: Sun Dec 07, 2008 10:22 pm    Post subject: compiling problem with WRFV3 Reply with quote

hi,

When I compile WRFV3 with pgf90,I got this error massage below


mpif90 -f90=pgf90 -c -r4 -i4 -O0 -w -Mfree -byteswapio -I../dyn_em -I../dyn_nmm -module /home/liliknn/Program/WRFV3/main -I/home/liliknn/Program/WRFV3/external/esmf_time_f90 -I/home/liliknn/Program/WRFV3/main -I/home/liliknn/Program/WRFV3/external/io_netcdf -I/home/liliknn/Program/WRFV3/external/io_int -I/home/liliknn/Program/WRFV3/frame -I/home/liliknn/Program/WRFV3/share -I/home/liliknn/Program/WRFV3/phys -I/home/liliknn/Program/WRFV3/chem -I/home/liliknn/Program/WRFV3/inc module_comm_dm.f90
pgf90-Info-Switch -fast forces -O2
pgf90-Fatal-/home/liliknn/Program/PGI/linux86/7.1-6/bin/newcg/pgf901 TERMINATED by signal 9
Arguments to /home/liliknn/Program/PGI/linux86/7.1-6/bin/newcg/pgf901
/home/liliknn/Program/PGI/linux86/7.1-6/bin/newcg/pgf901 module_comm_dm.f90 -opt 2 -terse 1 -inform severe -nohpf -nostatic -x 119 0x100000 -x 19 0x400000 -x 59 4 -x 15 2 -x 49 0x400004 -x 51 0x20 -x 57 0x4c -x 58 0x10000 -x 124 0x1000 -x 57 0xfb0000 -x 58 0x78031040 -x 70 0x6c00 -x 47 0x400000 -x 48 3328 -stdinc /home/liliknn/Program/PGI/linux86/7.1-6/include:/usr/local/include:/usr/lib/gcc/i386-redhat-linux/4.3.0/include:/usr/lib/gcc/i386-redhat-linux/4.3.0/include:/usr/include -def unix -def __unix -def __unix__ -def linux -def __linux -def __linux__ -def i386 -def __i386 -def __i386__ -def __NO_MATH_INLINES -def linux86 -def __THROW= -def __extension__= -def __SSE__ -def __MMX__ -def __SSE2__ -def __SSE3__ -idir ../dyn_em -idir ../dyn_nmm -idir /home/liliknn/Program/WRFV3/external/esmf_time_f90 -idir /home/liliknn/Program/WRFV3/main -idir /home/liliknn/Program/WRFV3/external/io_netcdf -idir /home/liliknn/Program/WRFV3/external/io_int -idir /home/liliknn/Program/WRFV3/frame -idir /home/liliknn/Program/WRFV3/share -idir /home/liliknn/Program/WRFV3/phys -idir /home/liliknn/Program/WRFV3/chem -idir /home/liliknn/Program/WRFV3/inc -idir /home/liliknn/Program/MPICH2/include -idir /home/liliknn/Program/MPICH2/include -freeform -i4 -x 125 2 -vect 48 -x 53 2 -y 124 0x8 -freeform -moddir /home/liliknn/Program/WRFV3/main -output /tmp/pgf90n2IbNrN-HRuy.ilm
make[2]: [module_comm_dm.o] error 127 (ignored)

My system is Fedora 9 32bit
MPICH2 1.0.8
4*P4 3.0G HT

Can you help me?

liliknn
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mkcolg



Joined: 30 Jun 2004
Posts: 6129
Location: The Portland Group Inc.

PostPosted: Mon Dec 08, 2008 2:32 pm    Post subject: Reply with quote

Hi liliknn,

A signal 9 means the process was killed by a user or by the OS. I've seen the OS kill processes that use too much memory but pgf901 only uses about 170Mb when compiling this file.

Does this error occur consistently? Do you have other processes running? What are your limits (in csh 'limit')?

- Mat
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liliknn



Joined: 26 Oct 2008
Posts: 3

PostPosted: Mon Dec 08, 2008 10:44 pm    Post subject: Reply with quote

Hello Mat,

thanks for your hint.I have tried 3 or 4 times,everytime it is the same error.And the building progress lasts a very long time about 12-24 hours.

my limits are these below
[root@node1 ~]# ulimit -a
core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 24552
max locked memory (kbytes, -l) 32
max memory size (kbytes, -m) unlimited
open files (-n) 1024
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 10240
cpu time (seconds, -t) unlimited
max user processes (-u) 1024
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited
[root@node1 ~]#

I will set "ulimit -s unlimited" and try again.


And another problem is generally the same,but the error messages are different

rm -f module_comm_dm.o
/mirror/WRFDA/tools/standard.exe module_comm_dm.F > module_comm_dm.b
/lib/cpp -C -P -I/mirror/WRFDA/inc -DEM_CORE=1 -DNMM_CORE=0 -DNMM_MAX_DIM=2600 -DCOAMPS_CORE=0 -DDA_CORE=1 -DEXP_CORE=0 -DIWORDSIZE=4 -DDWORDSIZE=8 -DRWORDSIZE=8 -DLWORDSIZE=4 -DNONSTANDARD_SYSTEM -DBUFR -DFFTPACK -DPROMOTE_FLOAT -DNONSTANDARD_SYSTEM -DNORESHAPE -DDM_PARALLEL -DNETCDF -DGRIB1 -DINTIO -DLIMIT_ARGS -DCONFIG_BUF_LEN=32768 -DMAX_DOMAINS_F=21 -DNMM_NEST=0 -I. -traditional module_comm_dm.b > module_comm_dm.f90
rm -f module_comm_dm.b
mpif90 -f90=pgf90 -c -r8 -i4 -O0 -w -Mfree -byteswapio -module /mirror/WRFDA/main -I/mirror/WRFDA/external/esmf_time_f90 -I/mirror/WRFDA/main -I/mirror/WRFDA/external/io_netcdf -I/mirror/WRFDA/external/io_int -I/mirror/WRFDA/frame -I/mirror/WRFDA/share -I/mirror/WRFDA/phys -I/mirror/WRFDA/chem -I/mirror/WRFDA/inc module_comm_dm.f90
pgf90-Info-Switch -fast forces -O2
PGF90-F-0007-Subprogram too large to compile at this optimization level (module_comm_dm.f90: 41502)
PGF90/x86 Linux 7.1-4: compilation aborted
make[2]: [module_comm_dm.o] error 2 (ignored)

It was captured when building WRF-var 3.0.1 code with PGI 7.14

Does this mean that I just need more physical memory?(Now it is 1.5G)
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mkcolg



Joined: 30 Jun 2004
Posts: 6129
Location: The Portland Group Inc.

PostPosted: Tue Dec 09, 2008 9:34 am    Post subject: Reply with quote

Hi liliknn,

Quote:
And the building progress lasts a very long time about 12-24 hours

Your limits look ok, though you may want to increase your stack size to unlimited else WRF may get a stack overflow at runtime.

While WRFv3 does takes some time to build, 12-24 hours seems a bit much. On my 64-bit Core2 system it only takes about an hour. My guess is that you don't have a lot of memory on this system and the compilers are swapping in memory (or just running out in the case of the signal 9). Do you have access to another system you could build on?

Quote:
PGF90-F-0007-Subprogram too large to compile at this optimization level (module_comm_dm.f90: 41502)

This is a general message which basically means that the compiler ran out of memory.

Although you have "-O0" on the compile line, it appears that your mpif90 script automatically sets the "-fast" flag. Edit your mpif90 script and remove "-fast". This should help reduce the amount of memory the compiler needs.

- Mat
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liliknn



Joined: 26 Oct 2008
Posts: 3

PostPosted: Thu Dec 11, 2008 7:23 am    Post subject: Reply with quote

Hi Mat,

Thank you.I will try to build WRF on some other systems which have more physical memory.

-liliknn
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