ABINIT Discussion Forums

Dear Developers and Users

I am new to Abinit and successfully configured Abinit-8.10.1 in CentOS-6.9 with the following command:

./configure --with-config-file="./marge.in"

The summary of the important options are:
* C compiler : gnu version 4.9
* Fortran compiler: gnu version 4.9
* architecture : intel xeon (64 bits)

* debugging : basic
* optimizations : standard

* OpenMP enabled : no (collapse: ignored)
* MPI enabled : yes
* MPI-IO enabled : yes
* GPU enabled : no (flavor: none)

* TRIO flavor = netcdf
* TIMER flavor = abinit (libs: ignored)
* LINALG flavor = netlib-fallback (libs: ignored)
* ALGO flavor = none (libs: ignored)
* FFT flavor = fftw3 (libs: user-defined)
* MATH flavor = none (libs: ignored)
* DFT flavor = libxc-fallback+atompaw-fallback

However, when I run the make command as 'make mj4 > make.log', it ends with the following internal compiler error:

m_spin_model_primitive.F90: In function ‘__final_m_spin_model_primitive_Spin_model_primitive_t’:
m_spin_model_primitive.F90:905:0: internal compiler error: in gfc_conv_descriptor_data_get, at fortran/trans-array.c:145
end module m_spin_model_primitive
^
0x5e3f78 gfc_conv_descriptor_data_get(tree_node*)
../.././gcc/fortran/trans-array.c:145
0x5e96bf gfc_array_deallocate(tree_node*, tree_node*, tree_node*, tree_node*, tree_node*, gfc_expr*)
../.././gcc/fortran/trans-array.c:5346
0x63698a gfc_trans_deallocate(gfc_code*)
../.././gcc/fortran/trans-stmt.c:5481
0x5e0e87 trans_code
../.././gcc/fortran/trans.c:1798
0x634661 gfc_trans_simple_do
../.././gcc/fortran/trans-stmt.c:1443
0x634661 gfc_trans_do(gfc_code*, tree_node*)
../.././gcc/fortran/trans-stmt.c:1606
0x5e0f4a trans_code
../.././gcc/fortran/trans.c:1748
0x60047b gfc_generate_function_code(gfc_namespace*)
../.././gcc/fortran/trans-decl.c:5653
0x5e2311 gfc_generate_module_code(gfc_namespace*)
../.././gcc/fortran/trans.c:1995
0x5a0045 translate_all_program_units
../.././gcc/fortran/parse.c:4940
0x5a0045 gfc_parse_file()
../.././gcc/fortran/parse.c:5150
0x5dd175 gfc_be_parse_file
../.././gcc/fortran/f95-lang.c:212
Please submit a full bug report,
with preprocessed source if appropriate.
Please include the complete backtrace with any bug report.
See <http://gcc.gnu.org/bugs.html> for instructions.
make[5]: *** [m_spin_model_primitive.o] Error 1
make[5]: Leaving directory `/data2/arindam/VASP/ABINIT/abinit-8.10.1/src/78_effpot'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory `/data2/arindam/VASP/ABINIT/abinit-8.10.1/src'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/data2/arindam/VASP/ABINIT/abinit-8.10.1'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/data2/arindam/VASP/ABINIT/abinit-8.10.1'
make[1]: *** [multi] Error 2
make[1]: Leaving directory `/data2/arindam/VASP/ABINIT/abinit-8.10.1'
make: *** [mj4] Error 2

Any suggestions to solve this issue, please? Herein, I have attached the configure (marge.in) and the error output (make.log) files.

Thank you very much.

Hi,

what is the output of this command :
the content of the make.log file is not relevant...

can you rerun the compilation with :
and post the make.stderr file

jmb

Dear Admin

Thank you for your kind response. As you instructed I have run "mpif90 --show", which returns

/home/arindam/anaconda3/bin/mpif90: line 376: x86_64-conda_cos6-linux-gnu-gfortran: command not found

I have tried the "make -j 8 > make.log 2> make.stderr" and herein attached the make.stderr file.

Thank you very much.

Sincerely
Arindam Sannyal

Hi,

Sorry, I made a typo in the command ( only one dash ! )
can you retry ?


In your marge.in file, there is :

with_mpi_prefix="/data2/arindam/VASP/openmpi-4.0.2"

Then, the output of the "mpif90 -show" command should be something like

> mpif90 -show
gfortran -I/data2/arindam/VASP/openmpi-4.0.2/include...

However, I see in your post :

/home/arindam/anaconda3/bin/mpif90: line 376: x86_64-conda_cos6-linux-gnu-gfortran: command not found

There is obviously a problem in your environment...

Dear Jean-Michel Beuken

As you instructed, I have changed the environment of my system. Now the "mpif90 -show" command returns the following output:

gfortran -I/data2/arindam/VASP/openmpi-4.0.2/include -pthread -I/data2/arindam/VASP/openmpi-4.0.2/lib -Wl,-rpath -Wl,/data2/arindam/VASP/openmpi-4.0.2/lib -Wl,--enable-new-dtags -L/data2/arindam/VASP/openmpi-4.0.2/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi

Then I have configured Abinit with the new environment, however, the make command ends with an error. Herein, I have attached the 'marge.in' and 'make.stderr' files for your kind consideration, Can you please help me to solve the problem.

Thank you very much for your support.

Sincerely
Arindam Sannyal