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module_first_rk_step_part2.f90 gfortran: fatal error: Terminated (killed) signal terminated program f951

I

israelmp

New member
Greetings, I have been fighting with this error for 4 weeks, I have tried countless configurations but invariably
SAME error occurs during compilation of module module_first_rk_step_part2.f90

--MISTAKE---
module_first_rk_step_part1.f90
gfortran: fatal error: Terminated (killed) signal terminated program f951
compilation terminated.
make[2]: [../configure.wrf:364: start_em.o] Error 1 (no effect)
rm -f module_first_rk_step_part2.o

--MISTAKE---
module_first_rk_step_part2.f90
gfortran: fatal error: Terminated (killed) signal terminated program f951
compilation terminated.
make[2]: [../configure.wrf:358: module_first_rk_step_part1.o] Error 1 (no effect)
rm -f solve_em.o

NOTE:

I have tried both on virtual machines and on physical computers:

Virtual: 4 cores + 4 GB ram + swap 1 GB
Virtual: 4 cores + 4 GB ram + 2 GB swap
Virtual: 4 cores + 4 GB ram + swap 4 GB
Virtual: 4 cores + 8 GB ram + swap 4 GB
Virtual: 4 cores + 8 GB ram + swap 8 GB

Physical Equipment:
CoreDuo 2 cores 4 threads + 4 GB ram + 1 GB swap; 256GB SSD
Core i3 hardware: 2 cores 4 threads + 4 GB ram + 1 GB swap; 256GB SSD

In all previous cases, the same error is always presented.

Used libraries:
  • netcdf-4.1.3
  • Jasper-1.900.1
  • libpng-1.2.50
  • zlib-1.2.7

Compilers:
  • gfortran --version GNU Fortran (Debian 10.2.1-6) 10.2.1 20210110
  • gcc --version gcc (Debian 10.2.1-6) 10.2.1 20210110
  • cpp --version cpp (Debian 10.2.1-6) 10.2.1 20210110
  • mpirun --version mpirun (Open MPI) 4.1.4
System:
  • Linux master 5.10.0-18-amd64 #1 SMP Debian 5.10.140-1 (2022-09-02) x86_64 GNU/Linux


Environment Variables:

export CC=gcc
export FC=gfortran
export CXX=g++
export F77=gfortran
export DIR=/home/israelmp/a/cluster/lib_ucar_edu
export FCFLAGS=-m64
export FFLAGS=-m64
export JASPERLIB=$DIR/grib2/lib
export JASPERINC=$DIR/grib2/include
export LDFLAGS=-L$DIR/grib2/lib
export CPPFLAGS=-I$DIR/grib2/include
export NETCDF=$DIR/netcdf
export PATH=$DIR/netcdf/bin:$PATH
export WRFIO_NCD_NO_LARGE_FILE_SUPPORT=1
export PATH=$DIR/openmpi/bin:$PATH
export MPAS_EXTERNAL_LIBS="-L$DIR/netcdf/lib -L$DIR/grib2/lib -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -ldl -lz"
export MPAS_EXTERNAL_INCLUDES="-I$DIR/netcdf/include -I$DIR/grib2/include"

Thanks in advance, any feedback is appreciated.
 
israelmp said:
Greetings, I have been fighting with this error for 4 weeks, I have tried countless configurations but invariably
SAME error occurs during compilation of module module_first_rk_step_part2.f90

--MISTAKE---
module_first_rk_step_part1.f90
gfortran: fatal error: Terminated (killed) signal terminated program f951
compilation terminated.
make[2]: [../configure.wrf:364: start_em.o] Error 1 (no effect)
rm -f module_first_rk_step_part2.o

--MISTAKE---
module_first_rk_step_part2.f90
gfortran: fatal error: Terminated (killed) signal terminated program f951
compilation terminated.
make[2]: [../configure.wrf:358: module_first_rk_step_part1.o] Error 1 (no effect)
rm -f solve_em.o

NOTE:

I have tried both on virtual machines and on physical computers:

Virtual: 4 cores + 4 GB ram + swap 1 GB
Virtual: 4 cores + 4 GB ram + 2 GB swap
Virtual: 4 cores + 4 GB ram + swap 4 GB
Virtual: 4 cores + 8 GB ram + swap 4 GB
Virtual: 4 cores + 8 GB ram + swap 8 GB

Physical Equipment:
CoreDuo 2 cores 4 threads + 4 GB ram + 1 GB swap; 256GB SSD
Core i3 hardware: 2 cores 4 threads + 4 GB ram + 1 GB swap; 256GB SSD

In all previous cases, the same error is always presented.

Used libraries:
  • netcdf-4.1.3
  • Jasper-1.900.1
  • libpng-1.2.50
  • zlib-1.2.7

Compilers:
  • gfortran --version GNU Fortran (Debian 10.2.1-6) 10.2.1 20210110
  • gcc --version gcc (Debian 10.2.1-6) 10.2.1 20210110
  • cpp --version cpp (Debian 10.2.1-6) 10.2.1 20210110
  • mpirun --version mpirun (Open MPI) 4.1.4
System:
  • Linux master 5.10.0-18-amd64 #1 SMP Debian 5.10.140-1 (2022-09-02) x86_64 GNU/Linux


Environment Variables:

export CC=gcc
export FC=gfortran
export CXX=g++
export F77=gfortran
export DIR=/home/israelmp/a/cluster/lib_ucar_edu
export FCFLAGS=-m64
export FFLAGS=-m64
export JASPERLIB=$DIR/grib2/lib
export JASPERINC=$DIR/grib2/include
export LDFLAGS=-L$DIR/grib2/lib
export CPPFLAGS=-I$DIR/grib2/include
export NETCDF=$DIR/netcdf
export PATH=$DIR/netcdf/bin:$PATH
export WRFIO_NCD_NO_LARGE_FILE_SUPPORT=1
export PATH=$DIR/openmpi/bin:$PATH
export MPAS_EXTERNAL_LIBS="-L$DIR/netcdf/lib -L$DIR/grib2/lib -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -ldl -lz"
export MPAS_EXTERNAL_INCLUDES="-I$DIR/netcdf/include -I$DIR/grib2/include"

Thanks in advance, any feedback is appreciated.
Click to expand...
 

Attachments

  • log.compile.txt
    36.6 KB · Views: 7
  • configure.wrf.txt
    20.9 KB · Views: 2
Hi,
It doesn't look like the compile log is the full log. There is no error - it just simply cuts off. Can you try to compile again, following these steps (from the top-level wrf directory):
1) ./clean -a
2) ./configure
3) ./compile em_real -j 1 >& log.compile

And then resend the log.compile and configure.wrf files? Thanks!
 
israelmp said:
Greetings, I have been fighting with this error for 4 weeks, I have tried countless configurations but invariably
SAME error occurs during compilation of module module_first_rk_step_part2.f90

--MISTAKE---
module_first_rk_step_part1.f90
gfortran: fatal error: Terminated (killed) signal terminated program f951
compilation terminated.
make[2]: [../configure.wrf:364: start_em.o] Error 1 (no effect)
rm -f module_first_rk_step_part2.o

--MISTAKE---
module_first_rk_step_part2.f90
gfortran: fatal error: Terminated (killed) signal terminated program f951
compilation terminated.
make[2]: [../configure.wrf:358: module_first_rk_step_part1.o] Error 1 (no effect)
rm -f solve_em.o

NOTE:

I have tried both on virtual machines and on physical computers:

Virtual: 4 cores + 4 GB ram + swap 1 GB
Virtual: 4 cores + 4 GB ram + 2 GB swap
Virtual: 4 cores + 4 GB ram + swap 4 GB
Virtual: 4 cores + 8 GB ram + swap 4 GB
Virtual: 4 cores + 8 GB ram + swap 8 GB

Physical Equipment:
CoreDuo 2 cores 4 threads + 4 GB ram + 1 GB swap; 256GB SSD
Core i3 hardware: 2 cores 4 threads + 4 GB ram + 1 GB swap; 256GB SSD

In all previous cases, the same error is always presented.

Used libraries:
  • netcdf-4.1.3
  • Jasper-1.900.1
  • libpng-1.2.50
  • zlib-1.2.7

Compilers:
  • gfortran --version GNU Fortran (Debian 10.2.1-6) 10.2.1 20210110
  • gcc --version gcc (Debian 10.2.1-6) 10.2.1 20210110
  • cpp --version cpp (Debian 10.2.1-6) 10.2.1 20210110
  • mpirun --version mpirun (Open MPI) 4.1.4
System:
  • Linux master 5.10.0-18-amd64 #1 SMP Debian 5.10.140-1 (2022-09-02) x86_64 GNU/Linux


Environment Variables:

export CC=gcc
export FC=gfortran
export CXX=g++
export F77=gfortran
export DIR=/home/israelmp/a/cluster/lib_ucar_edu
export FCFLAGS=-m64
export FFLAGS=-m64
export JASPERLIB=$DIR/grib2/lib
export JASPERINC=$DIR/grib2/include
export LDFLAGS=-L$DIR/grib2/lib
export CPPFLAGS=-I$DIR/grib2/include
export NETCDF=$DIR/netcdf
export PATH=$DIR/netcdf/bin:$PATH
export WRFIO_NCD_NO_LARGE_FILE_SUPPORT=1
export PATH=$DIR/openmpi/bin:$PATH
export MPAS_EXTERNAL_LIBS="-L$DIR/netcdf/lib -L$DIR/grib2/lib -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -ldl -lz"
export MPAS_EXTERNAL_INCLUDES="-I$DIR/netcdf/include -I$DIR/grib2/include"

Thanks in advance, any feedback is appreciated.
Click to expand...

Greetings, I couldn't solve the problem, however, I downgraded from debian 11.5 to debian 10.13 and successfully compiled with the updated libraries,

==================================================== =========================
build started: Wed Oct 12 17:28:31 CDT 2022
construction completed: Wed Oct 12 17:40:43 CDT 2022

---> Executables created successfully <---

-rwxr-xr-x 1 39653544 Oct 12 17:40 main/ndown.exe
-rwxr-xr-x 1 39563512 Oct 12 17:40 main/real.exe
-rwxr-xr-x 1 39006520 Oct 12 17:40 main/tc.exe
-rwxr-xr-x 1 43995000 Oct 12 17:39 main/wrf.exe

==================================================== =========================

wrf-v4.4.1
jasper-1.900.1.tar.gz
libpng-1.6.38.tar.gz
netcdf-c-4.9.0.tar.gz
netcdf-fortran-4.6.0.tar.gz
szip-2.1.1.tar.gz
zlib-1.2.12.tar.gz
 
Hi, That is good to know! It seems to perhaps be related to the Linux version. This information may help others, so thank you for the update!
 
Hi,I have the same problem ！

wrf-v4.4.1 or wrf-4.3.3

GNU Fortran (GCC) 10.2.1 20210130 (Red Hat 10.2.1-11)
g++ (GCC) 10.2.1 20210130 (Red Hat 10.2.1-11)
gcc (GCC) 10.2.1 20210130 (Red Hat 10.2.1-11)



Thanks
 

Attachments

  • compile.log
    920.2 KB · Views: 3
  • configure.wrf.txt
    20.6 KB · Views: 1
@snow
When you compiled, did you use ">&" in the command? Although the log says there are errors, there are none listed, which makes me think the standard error wasn't included with the output. Can you issue the following?

./clean -a
./configure
./compile em_real -j 1 >& compile.log

and then send me that new log? Thanks!
 
kwerner said:
@snow
When you compiled, did you use ">&" in the command? Although the log says there are errors, there are none listed, which makes me think the standard error wasn't included with the output. Can you issue the following?

./clean -a
./configure
./compile em_real -j 1 >& compile.log

and then send me that new log? Thanks!
Click to expand...
Hi，thank you for your reply，I followed your instructions to generate a new log file，but the content is the same. Where can I see the errors？
 

Attachments

  • compile.log
    920 KB · Views: 1
Hi,
If you're certain you used the ">&" syntax in the compile command, could it be that "Error" is not in English in the compile log? We need to search for the first instance of "Error" with a capital "E."
Code: 
grep Error compile.log
Unfortunately I'm not able to read anything but English. If you see it anywhere in the log file, perhaps you can paste the error in your response message and let me know which line it's on. Thanks!
 
kwerner said:
Hi,
If you're certain you used the ">&" syntax in the compile command, could it be that "Error" is not in English in the compile log? We need to search for the first instance of "Error" with a capital "E."
Code: 
grep Error compile.log
Unfortunately I'm not able to read anything but English. If you see it anywhere in the log file, perhaps you can paste the error in your response message and let me know which line it's on. Thanks!
Click to expand...
Hi，I have changed the language of my system，and re-executed the program. Thx again！
 

Attachments

  • compile.log
    920.2 KB · Views: 1
Hi,
Thanks for doing that. I'm able to find several errors, but since you compiled the code with 4 processors, it's difficult to determine which error is the one causing the additional errors. Can you try to compile one more time, making sure to clean the code first (clean -a), then when you compile, make sure to set "-j 1" so that it only uses one processor to compile.
Code: 
./compile em_real -j 1 >& compile.log

Then send me those files again, and please set the language to English so I can read the new files. I expect that it will fail again, so when it does, send me the new compile log and your configure.wrf file. Thanks!
 
kwerner said:
Hi,
Thanks for doing that. I'm able to find several errors, but since you compiled the code with 4 processors, it's difficult to determine which error is the one causing the additional errors. Can you try to compile one more time, making sure to clean the code first (clean -a), then when you compile, make sure to set "-j 1" so that it only uses one processor to compile.
Code: 
./compile em_real -j 1 >& compile.log

Then send me those files again, and please set the language to English so I can read the new files. I expect that it will fail again, so when it does, send me the new compile log and your configure.wrf file. Thanks!
Click to expand...
Hi, Thank you for your patient reply.
I regenerated the compiled file according to your instructions，please see the attachment.
 

Attachments

  • compile.log
    872.5 KB · Views: 3
  • configure.wrf.txt
    20.8 KB · Views: 4
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