No YAML Error found abinit-9.2.2 [SOLVED]
Posted: Thu Dec 03, 2020 5:04 pm
Dear developers,
I compiled the latest version of abinit-9.2.2 using the following configure file.
# installation location
prefix=/home/nsingh3/.local
CC='mpicc'
CXX="mpiCC"
FC="mpif90"
# MPI settings
with_mpi="yes"
enable_mpi_io="yes"
# linear algebra settings
with_linalg_flavor="openblas"
LINALG_LIBS="-L/usr/lib64 -lopenblas"
# mandatory libraries
with_hdf5="yes"
with_netcdf="yes"
with_netcdf_fortran="yes"
with_libxc="yes"
# FFT flavor
with_fft_flavor="fftw3"
FFTW3_LIBS="-L/usr/lib64 -lfftw3 -lfftw3f"
with_libxml2="yes"
LIBXML2_LIBS="-L/usr/include/libxml2/libxml/ -lxmlf90"
with_libyaml="yes"
LIBYAML_LIBS="/sw/arch/RedHatEnterpriseServer7/EB_production/2020/software/libyaml/0.2.2-GCCcore-9.3.0/lib/libyaml.a"
with_libpsml="yes"
LIBPSML_LIBS="/home/nsingh3/.local/lib/libpsml.a"
with_xmlf90="yes"
XMLF90_FCFLAGS="-I/home/nsingh3/.local/include"
XMLF90_LIBS="-L/home/nsingh3/.local/lib/ -lxmlf90"
# Enable Netcdf mode in Abinit (use netcdf as default I/O library)
enable_netcdf_default="yes"
enable_openmp="yes"
It sucessfully made the abinit executable but when do tests then I get the following error.
Command /lustre1/0/einf581/abinit-9.2.2/build/src/98_main/abinit < /lustre1/0/einf581/abinit-9.2.2/build/tests/Test_suite/v1_t01/t01.stdin > /lustre1/0/einf581/abinit-9.2.2/build/tests/Test_suite/v1_t01/t01.stdout 2> /lustre1/0/einf581/abinit-9.2.2/build/tests/Test_suite/v1_t01/t01.stderr
returned exit_code: 34
[v1][t01][np=1][run_etime: 1.59 s]: fldiff fatal error:
file 1 has more significant lines than file 2 (435 > 0).
[file=t01.out]
[v1][t01][np=1] Test was not expected to fail but subprocesses returned retcode: 34
[int2:18891] *** An error occurred in MPI_Info_dup
[int2:18891] *** reported by process [3692756993,0]
[int2:18891] *** on communicator MPI_COMM_WORLD
[int2:18891] *** MPI_ERR_INFO: invalid info object
[int2:18891] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
[int2:18891] *** and potentially your MPI job)
No YAML Error found in: [v1][t01][np=1]
Suite failed passed succeeded skipped disabled run_etime tot_etime
v1 1 0 0 0 0 1.59 1.64
Completed in 1.81 [s]. Average time for test=1.59 [s], stdev=0.00 [s]
Summary: failed=1, succeeded=0, passed=0, skipped=0, disabled=0
Execution completed.
I am attaching the config.log file.
I have tried to link libyaml both dynamically and statistically. But gives the same error.
Any help would be appreciated.
I compiled the latest version of abinit-9.2.2 using the following configure file.
# installation location
prefix=/home/nsingh3/.local
CC='mpicc'
CXX="mpiCC"
FC="mpif90"
# MPI settings
with_mpi="yes"
enable_mpi_io="yes"
# linear algebra settings
with_linalg_flavor="openblas"
LINALG_LIBS="-L/usr/lib64 -lopenblas"
# mandatory libraries
with_hdf5="yes"
with_netcdf="yes"
with_netcdf_fortran="yes"
with_libxc="yes"
# FFT flavor
with_fft_flavor="fftw3"
FFTW3_LIBS="-L/usr/lib64 -lfftw3 -lfftw3f"
with_libxml2="yes"
LIBXML2_LIBS="-L/usr/include/libxml2/libxml/ -lxmlf90"
with_libyaml="yes"
LIBYAML_LIBS="/sw/arch/RedHatEnterpriseServer7/EB_production/2020/software/libyaml/0.2.2-GCCcore-9.3.0/lib/libyaml.a"
with_libpsml="yes"
LIBPSML_LIBS="/home/nsingh3/.local/lib/libpsml.a"
with_xmlf90="yes"
XMLF90_FCFLAGS="-I/home/nsingh3/.local/include"
XMLF90_LIBS="-L/home/nsingh3/.local/lib/ -lxmlf90"
# Enable Netcdf mode in Abinit (use netcdf as default I/O library)
enable_netcdf_default="yes"
enable_openmp="yes"
It sucessfully made the abinit executable but when do tests then I get the following error.
Command /lustre1/0/einf581/abinit-9.2.2/build/src/98_main/abinit < /lustre1/0/einf581/abinit-9.2.2/build/tests/Test_suite/v1_t01/t01.stdin > /lustre1/0/einf581/abinit-9.2.2/build/tests/Test_suite/v1_t01/t01.stdout 2> /lustre1/0/einf581/abinit-9.2.2/build/tests/Test_suite/v1_t01/t01.stderr
returned exit_code: 34
[v1][t01][np=1][run_etime: 1.59 s]: fldiff fatal error:
file 1 has more significant lines than file 2 (435 > 0).
[file=t01.out]
[v1][t01][np=1] Test was not expected to fail but subprocesses returned retcode: 34
[int2:18891] *** An error occurred in MPI_Info_dup
[int2:18891] *** reported by process [3692756993,0]
[int2:18891] *** on communicator MPI_COMM_WORLD
[int2:18891] *** MPI_ERR_INFO: invalid info object
[int2:18891] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
[int2:18891] *** and potentially your MPI job)
No YAML Error found in: [v1][t01][np=1]
Suite failed passed succeeded skipped disabled run_etime tot_etime
v1 1 0 0 0 0 1.59 1.64
Completed in 1.81 [s]. Average time for test=1.59 [s], stdev=0.00 [s]
Summary: failed=1, succeeded=0, passed=0, skipped=0, disabled=0
Execution completed.
I am attaching the config.log file.
I have tried to link libyaml both dynamically and statistically. But gives the same error.
Any help would be appreciated.