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pgf902 TERMINATED by signal 11
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cjo_100



Joined: 27 Feb 2014
Posts: 5

PostPosted: Thu Feb 27, 2014 10:31 am    Post subject: pgf902 TERMINATED by signal 11 Reply with quote

Hi

I tried compiling WRF with the PGI compilers 14.1. The compilation worked without any problems with 10.6. With 14.1 I get the error message

pgf902 TERMINATED by signal 11

What is the appropriate course of action in this case?

J
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mkcolg



Joined: 30 Jun 2004
Posts: 6125
Location: The Portland Group Inc.

PostPosted: Thu Feb 27, 2014 2:50 pm    Post subject: Reply with quote

Hi J,

Quote:
What is the appropriate course of action in this case?
Let me try and recreate the problem here. What version of WRF are you using? Are you using another package (like WRF-CHEM)? At what file does the error occur?

Thanks,
Mat
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cjo_100



Joined: 27 Feb 2014
Posts: 5

PostPosted: Thu Feb 27, 2014 6:26 pm    Post subject: Reply with quote

Hi Mat

The problem occurs with WRF-CHEM 3.1.1 and 3.5 (no modifications). I didn't test other versions. The compilation fails at

mpif90 -o module_mosaic_addemiss.o -c -O2 -w -Mfree -Mextend -byteswapio -tp amd64 -Kieee -Mpreprocess -Msave -DFC=PGI -I../dyn_em -I../dyn_nmm -module /home/user/WRF3.5/main -I/home/user/WRF3.5/external/esmf_time_f90 -I/home/user/WRF3.5/main -I/home/user/WRF3.5/external/io_netcdf -I/home/user/WRF3.5/external/io_int -I/home/user/WRF3.5/frame -I/home/user/WRF3.5/share -I/home/user/WRF3.5/phys -I/home/user/WRF3.5/chem -I/home/user/WRF3.5/inc -I/usr/local/netCDF/netcdf-4.0-pgi/include -r4 -i4 module_mosaic_addemiss.f90

pgf90-Fatal-/opt/pgi/linux86-64/14.1/bin/pgf902 TERMINATED by signal 11

Arguments to /opt/pgi/linux86-64/14.1/bin/pgf902
/opt/pgi/linux86-64/14.1/bin/pgf902 /tmp/pgf90ZvjbzbYIsjA9.ilm -fn module_mosaic_addemiss.f90 -opt 2 -terse 1 -inform severe -x 51 0x20 -x 119 0xa10000 -x 122 0x40 -x 123 0x1000 -x 127 4 -x 127 17 -x 19 0x400000 -x 28 0x40000 -x 120 0x10000000 -x 70 0x8000 -x 122 1 -x 125 0x20000 -x 117 0x1000 -quad -vect 56 -y 34 16 -x 34 0x8 -y 19 8 -y 35 0 -x 42 0x30 -x 39 0x40 -x 39 0x80 -x 34 0x400000 -x 149 1 -x 150 1 -x 59 4 -x 6 0x100 -y 129 2 -tp k8 -x 120 0x1000 -x 124 0x1400 -y 15 2 -x 57 0x3b0000 -x 58 0x48000000 -x 49 0x100 -x 120 0x200 -astype 0 -x 121 1 -ieee 1 -save -x 124 1 -y 189 0x4000000 -x 9 1 -x 72 0x1 -x 136 0x11 -quad -x 119 0x10000000 -x 129 0x40000000 -x 164 0x1000 -x 42 0x400000 -y 129 4 -x 129 0x400 -y 124 0x8 -cmdline '+pgf90 module_mosaic_addemiss.f90 -tp amd64 -o module_mosaic_addemiss.o -c -O2 -Mvect=sse -Mcache_align -Mpre -w -Mfree -Mextend -byteswapio -Kieee -Mpreprocess -Msave -DFC=PGI -I../dyn_em -I../dyn_nmm -module /home/user/WRF3.5/main -I/home/user/WRF3.5/external/esmf_time_f90 -I/home/user/WRF3.5/main -I/home/user/WRF3.5/external/io_netcdf -I/home/user/WRF3.5/external/io_int -I/home/user/WRF3.5/frame -I/home/user/WRF3.5/share -I/home/user/WRF3.5/phys -I/home/user/WRF3.5/chem -I/home/user/WRF3.5/inc -I/usr/local/netCDF/netcdf-4.0-pgi/include -r4 -i4 -I/usr/local/openMPI/openmpi-1.6.4-pgi/include -I/usr/local/openMPI/openmpi-1.6.4-pgi/lib' -asm /tmp/pgf907vjbX1reKK5Q.sm

Thanks for your response!

J
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David Norton



Joined: 18 Aug 2004
Posts: 20

PostPosted: Mon Mar 03, 2014 7:26 pm    Post subject: Reply with quote

Hi J -

I have not yet been able to reproduce your issue.

I've taken WRFV3.5.1 and untarred it. WRFV3-Chem-3.5.1 and untarred it and moved the resulting chem directory into WRFV3.

Did a "./clean -a"

set the environment variables:
setenv WRF_CHEM 1
setenv EM_CORE 1
setenv NMM_CORE 0

configured and chose option 7 (PGI distributed memory build)

compiled with PGI 14.1 on both an Intel machine and an AMD machine

I'm not seeing the issue you report.

Would you be able to provide more details of how you set up the environment and configured the model to help me track down the issue you are seeing?

thanks
-dave


rm -f module_mosaic_addemiss.o
/lib/cpp -C -P -I/home/norton/Documents/NCAR/WRF/WRFV3/inc -DEM_CORE=1 -DNMM_CORE=0 -DNMM_MAX_DIM=2600 -DCOAMPS_CORE=0 -DDA_CORE=0 -DEXP_CORE=0 -DIWORDSIZE=4 -DDWORDSIZE=8 -DRWORDSIZE=4 -DLWORDSIZE=4 -DNONSTANDARD_SYSTEM_SUBR -DWRF_USE_CLM -DDM_PARALLEL -DNETCDF -DUSE_ALLO\
CATABLES -DGRIB1 -DINTIO -DLIMIT_ARGS -DCONFIG_BUF_LEN=65536 -DMAX_DOMAINS_F=21 -DMAX_HISTORY=25 -DNMM_NEST=0 -DWRF_CHEM -DBUILD_CHEM=1 -I. -traditional module_mosaic_addemiss.F > module_mosaic_addemiss.bb
/home/norton/Documents/NCAR/WRF/WRFV3/tools/standard.exe module_mosaic_addemiss.bb | /lib/cpp -C -P > module_mosaic_addemiss.f90
rm -f module_mosaic_addemiss.b module_mosaic_addemiss.bb
mpif90 -f90=pgf90 -o module_mosaic_addemiss.o -c -O3 -w -Mfree -byteswapio -I../dyn_em -I../dyn_nmm -module /home/norton/Documents/NCAR/WRF/WRFV3/main -I/home/norton/Documents/NCAR/WRF/WRFV3/external/esmf_time_f90 -I/home/norton/Documents/NCAR/WRF/WRFV3/main -I/home/n\
orton/Documents/NCAR/WRF/WRFV3/external/io_netcdf -I/home/norton/Documents/NCAR/WRF/WRFV3/external/io_int -I/home/norton/Documents/NCAR/WRF/WRFV3/frame -I/home/norton/Documents/NCAR/WRF/WRFV3/share -I/home/norton/Documents/NCAR/WRF/WRFV3/phys -I/home/norton/Documents/NCAR/W\
RF/WRFV3/chem -I/home/norton/Documents/NCAR/WRF/WRFV3/inc -I/proj/ta/libraries/netcdf-fortran-4.2/linux86-64/pgi/14.1/redhat-5.3-Tikanga/include -r4 -i4 module_mosaic_addemiss.f90
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cjo_100



Joined: 27 Feb 2014
Posts: 5

PostPosted: Wed Mar 05, 2014 4:49 pm    Post subject: Reply with quote

Hi Dave

I forgot to mention that I use gcc instead of pgcc to compile the C parts of the WRF/Chem code. This has worked so far with the 10.6 version of pgf90. The problem I experience can be reproduced as follows (Fedora Linux 3.11.10-100.fc18.x86_64 on an AMD Opteron(tm) processor 6376):

Downloaded WRFV3.5.1, untarred it; downloaded WRFV3-Chem-3.5.1, untarred it, moved the resulting chem directory into WRFV3. Renamed WRFV3 to WRF3.5.1 to distinguish from older versions. Then (using the bash):

./clean -a

export LM_LICENSE_FILE=$LM_LICENSE_FILE:/opt/pgi/license.dat
export PATH=/opt/pgi/linux86-64/14.1/bin:$PATH

cd WRF3.5.1
WRF_ROOT=`pwd`
export PATH=$PATH:.
export PATH=$PATH:${WRF_ROOT}/chem/KPP/util/wkc
export WRF_EM_CORE=1
export WRF_NMM_CORE=0
export WRFIO_NCD_LARGE_FILE_SUPPORT=1
export WRF_CHEM=1
export WRF_KPP=1
export YACC='yacc -d'
export MPI=/usr/local/openMPI/openmpi-1.6.4-pgi
export PATH=${MPI}/bin/:$PATH
export NETCDF=/usr/local/netCDF/netcdf-4.0-pgi
export FLEX=${HOME}/Packages/flex/flex-2.5.3/bin/flex
export FLEX_LIB_DIR=${HOME}/Packages/flex/flex-2.5.3/lib

To compile with pgf90 and gcc, I add the following section at the end of ${WRF_ROOT}/arch/configure_new.defaults:

###########################################################
#ARCH Linux x86_64, PGI compiler with gcc #serial smpar dmpar dm+sm
#
DMPARALLEL = # 1
OMPCPP = # -D_OPENMP
OMP = # -mp -Minfo=mp
SFC = pgf90
SCC = gcc
DM_FC = mpif90
DM_CC = mpicc
FC = CONFIGURE_FC
CC = CONFIGURE_CC
CCOMP = CONFIGURE_CC
LD = $(FC)
RWORDSIZE = CONFIGURE_RWORDSIZE
PROMOTION = -r$(RWORDSIZE) -i4
ARCH_LOCAL = -DNONSTANDARD_SYSTEM_SUBR
CFLAGS_LOCAL = -w -O3 -m64
LDFLAGS_LOCAL =
CPLUSPLUSLIB =
ESMF_LDFLAG = $(CPLUSPLUSLIB)
FCOPTIM = -O2
FCREDUCEDOPT = $(FCOPTIM)
FCNOOPT = -O0
OPTERON_TYPE = -tp amd64
FCDEBUG = # -C -g $(FCNOOPT)
FORMAT_FIXED = -Mfixed
FORMAT_FREE = -Mfree -Mextend
FCSUFFIX =
BYTESWAPIO = -byteswapio
FCBASEOPTS = -w $(FCDEBUG) $(FORMAT_FREE) $(BYTESWAPIO) $(OPTERON_TYPE) -Kieee -Mpreprocess -Msave -DFC=PGI
MODULE_SRCH_FLAG = -module $(WRF_SRC_ROOT_DIR)/main
TRADFLAG = -traditional
CPP = /lib/cpp -C -P
AR = ar
ARFLAGS = ru
M4 = m4 -B 14000
RANLIB = ranlib
CC_TOOLS = $(SCC)

Then I run ./configure, choose options 58

"Linux x86_64, PGI compiler with gcc (dmpar)"

and then option 1, followed by

./compile em_real 2>&1 | tee compile.em_real.log

J
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