An error occurred while running abinit without root privilege.

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poltast
Posts: 2
Joined: Tue Mar 03, 2020 3:26 am

An error occurred while running abinit without root privilege.

Post by poltast » Tue Mar 03, 2020 3:52 am

Hi,
As I mentioned on subject, I faced a trouble on my tutorial.

I'm just trying to run the test code (tutorial 1 , molecular hydrogen case) without root privilege and encounter error below in err file.

*** The MPI_Comm_f2c() function was called before MPI_INIT was invoked.
*** This is disallowed by the MPI standard.
*** Your MPI job will now abort.
[localhost.localdomain:06854] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!


When I run this code with root privilege, there was no err message in err file and I already passed the running tests using runtests.py code(actually running test codes were done with root privilege).

I though it was kind of environmental problem related to library and added library paths from abinit directory but it does not work at all. How can I solve this problem?

OS: centos 8.1
aninit: 8.10.2

Thank you for reading my post!

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jbeuken
Posts: 346
Joined: Tue Aug 18, 2009 9:24 pm
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Re: An error occurred while running abinit without root privilege.

Post by jbeuken » Tue Mar 03, 2020 5:15 pm

Hi,

Is it repeatable?

Which MPI package ( MPICH, OpenMPI ) did you use and which version?

Which compiler ?

jmb
------
Jean-Michel Beuken
Computer Scientist

poltast
Posts: 2
Joined: Tue Mar 03, 2020 3:26 am

Re: An error occurred while running abinit without root privilege.

Post by poltast » Wed Mar 04, 2020 2:39 am

Thank you for replying to my post,

Yes it is repeatable and I use MPICH 3.3.2.

And if I use mpi run option like "mpirun -n 2 abinit < tbase1_x.files > log 2> err", results are


At line 1363 of file ../../../src/55_abiutil/m_dtfil.F90 (unit = 5, file = 'stdin')
Fortran runtime error: End of file

Error termination. Backtrace:
*** The MPI_Comm_f2c() function was called before MPI_INIT was invoked.
*** This is disallowed by the MPI standard.
*** Your MPI job will now abort.
[localhost.localdomain:19937] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
#0 0x7f4c58188131 in ???
#1 0x7f4c58188cd9 in ???
#2 0x7f4c581894e1 in ???
#3 0x7f4c5838e77b in ???
#4 0x7f4c5838ed72 in ???
#5 0x7f4c5838ba6b in ???
#6 0x7f4c58390484 in ???
#7 0x7f4c583912f4 in ???
#8 0xf72d34 in __m_dtfil_MOD_iofn1
at ../../../src/55_abiutil/m_dtfil.F90:1363
#9 0x406f78 in abinit
at ../../../src/98_main/abinit.F90:251
#10 0x406cae in main
at ../../../src/98_main/abinit.F90:94
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

Process name: [[40275,1],0]
Exit code: 1
--------------------------------------------------------------------------


Because running mpi with root privilege is blocked by policy, I can not test it with root privilege.

Thank you!

poltast

P.S.
I forgot to mention the compiler.
Below are details on my build.
=== Build Information ===
Version : 8.10.2
Build target : x86_64_linux_gnu8.3
Build date : 20200229

=== Compiler Suite ===
C compiler : gnu8.3
C++ compiler : gnu8.3
Fortran compiler : gnu8.3
CFLAGS : -m64 -g -O2 -mtune=native -march=native -fPIC
CXXFLAGS : -m64 -g -O2 -mtune=native -march=native -fPIC
FCFLAGS : -m64 -g -ffree-line-length-none -fPIC
FC_LDFLAGS :

=== Optimizations ===
Debug level : basic
Optimization level : standard
Architecture : unknown_unknown

=== Multicore ===
Parallel build : yes
Parallel I/O : yes
openMP support : no
GPU support : no

=== Connectors / Fallbacks ===
Connectors on : yes
Fallbacks on : yes
DFT flavor : libxc-fallback+atompaw-fallback+bigdft-fallback+wannier90-fallback
FFT flavor : fftw3
LINALG flavor : atlas
MATH flavor : none
TIMER flavor : abinit
TRIO flavor : netcdf

=== Experimental features ===
Bindings : @enable_bindings@
Exports : yes
GW double-precision : yes

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