Internal compiler error of Abinit-8.10.1 in CentOS 6.9

ornis · Post by **ornis** » Fri Nov 22, 2019 11:30 am

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.

Post by **admin** » Fri Nov 22, 2019 1:59 pm

Hi,

what is the output of this command :

Code: Select all

mpif90 --show

the content of the make.log file is not relevant...

can you rerun the compilation with :

Code: Select all

make -j 8 > make.log 2> make.stderr

and post the make.stderr file

jmb

ornis · Post by **ornis** » Mon Nov 25, 2019 4:29 am

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

Post by **jbeuken** » Mon Nov 25, 2019 10:16 am

Hi,

Sorry, I made a typo in the command ( only one dash ! )

Code: Select all

mpif90 -show

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...

ornis · Post by **ornis** » Tue Nov 26, 2019 8:14 am

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

ABINIT Discussion Forums

Internal compiler error of Abinit-8.10.1 in CentOS 6.9

Internal compiler error of Abinit-8.10.1 in CentOS 6.9

Re: Internal compiler error of Abinit-8.10.1 in CentOS 6.9

Re: Internal compiler error of Abinit-8.10.1 in CentOS 6.9

Re: Internal compiler error of Abinit-8.10.1 in CentOS 6.9

Re: Internal compiler error of Abinit-8.10.1 in CentOS 6.9