Segmentation fault - invalid memory reference error in abinit-8.10.3 when running ground state calculation  [SOLVED]

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shivaprasad
Posts: 5
Joined: Fri Aug 07, 2020 8:09 pm

Segmentation fault - invalid memory reference error in abinit-8.10.3 when running ground state calculation  [SOLVED]

Post by shivaprasad » Sat Aug 08, 2020 8:08 pm

Dear abinit users and developers,

I have configured and compiled abinit -8.10.3 in a HPC-cluster running Cent OS 7. Abinit is configured with below configuration file. I am using Intel parallel_studio_xe_2019 update 4 cluster edition.
n199.ac:

Code: Select all

FC="mpif90"
CC="mpicc"
CXX="mpicxx"
enable_mpi="yes"
enable_openmp="yes"
enable_mpi-io="yes"
with_tardir="/home/shiva/.abinit/tarballs"
enable_fallbacks="yes"
with_trio_flavor="netcdf"
with_fft_flavor="fftw3"
with_linalg_flavor="mkl" 
with_dft_flavor="libxc" 
The netcdf version 4.1.1 is and libxc version 3.0.0 are used.

The abinit program was configured and compiled without any error message. But, when I try to run the Si calculation I am getting "Program received signal SIGSEGV: Segmentation fault - invalid memory reference" error and the program stops. The err file shows the below message:

Code: Select all

libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x2B44CA4C5697
#1  0x2B44CA4C5CDE
#2  0x2B44CC83B3AF
#3  0x2B455CE4AB76
#0  0x2B7104E85697
#4  0x2B44C61EF7A2
#1  0x2B7104E85CDE
#5  0x2B44C4051DC5#2  0x2B71071FB3AF

#3  0x2B719780AB76
#4  0x2B7100BAF7A2
#5  0x2B70FEA11DC5

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x2B51FEC3C697
#1  0x2B51FEC3CCDE
#2  0x2B5200FB23AF
#3  0x2B52915C1B76
#4  0x2B51FA9667A2
#5  0x2B51F87C8DC5
#0  0x2B0B7F1E5697
#1  0x2B0B7F1E5CDE
#2  0x2B0B8155B3AF
#3  0x2B0C11B6AB76
#4  0x2B0B7AF0F7A2
#5  0x2B0B78D71DC5
#6  0x1192FC1 in __m_cgtools_MOD_cg_zdotc at m_cgtools.F90:728
#6  0x1192FC1 in __m_cgtools_MOD_cg_zdotc at m_cgtools.F90:728
#7  0x1193170 in __m_cgtools_MOD_dotprod_g at m_cgtools.F90:1364
#7  0x1193170 in __m_cgtools_MOD_dotprod_g at m_cgtools.F90:1364
#8  0xAA4FF3 in __m_cgwf_MOD_cgwf at m_cgwf.F90:499
#8  0xAA4FF3 in __m_cgwf_MOD_cgwf at m_cgwf.F90:499
#9  0x598482 in __m_vtowfk_MOD_vtowfk at m_vtowfk.F90:408
#9  0x598482 in __m_vtowfk_MOD_vtowfk at m_vtowfk.F90:408
#6  0x1192FC1 in __m_cgtools_MOD_cg_zdotc at m_cgtools.F90:728
#7  0x1193170 in __m_cgtools_MOD_dotprod_g at m_cgtools.F90:1364
#6  0x1192FC1 in __m_cgtools_MOD_cg_zdotc at m_cgtools.F90:728
#7  0x1193170 in __m_cgtools_MOD_dotprod_g at m_cgtools.F90:1364
#10  0x57D7B6 in __m_vtorho_MOD_vtorho at m_vtorho.F90:943
#10  0x57D7B6 in __m_vtorho_MOD_vtorho at m_vtorho.F90:943
#8  0xAA4FF3 in __m_cgwf_MOD_cgwf at m_cgwf.F90:499
#8  0xAA4FF3 in __m_cgwf_MOD_cgwf at m_cgwf.F90:499
#9  0x598482 in __m_vtowfk_MOD_vtowfk at m_vtowfk.F90:408
#9  0x598482 in __m_vtowfk_MOD_vtowfk at m_vtowfk.F90:408
#11  0x5475C4 in __m_scfcv_core_MOD_scfcv_core at m_scfcv_core.F90:1536
#10  0x57D7B6 in __m_vtorho_MOD_vtorho at m_vtorho.F90:943
#11  0x5475C4 in __m_scfcv_core_MOD_scfcv_core at m_scfcv_core.F90:1536
#12  0x53B3D4 in __m_scfcv_MOD_scfcv_scfcv at m_scfcv.F90:746
#10  0x57D7B6 in __m_vtorho_MOD_vtorho at m_vtorho.F90:943
#12  0x53B3D4 in __m_scfcv_MOD_scfcv_scfcv at m_scfcv.F90:746
#11  0x5475C4 in __m_scfcv_core_MOD_scfcv_core at m_scfcv_core.F90:1536
#13  0x52B453 in __m_gstate_MOD_gstate at m_gstate.F90:1331
#11  0x5475C4 in __m_scfcv_core_MOD_scfcv_core at m_scfcv_core.F90:1536
#12  0x53B3D4 in __m_scfcv_MOD_scfcv_scfcv at m_scfcv.F90:746
#14  0x428A09 in __m_gstateimg_MOD_gstateimg at m_gstateimg.F90:566
#13  0x52B453 in __m_gstate_MOD_gstate at m_gstate.F90:1331
#12  0x53B3D4 in __m_scfcv_MOD_scfcv_scfcv at m_scfcv.F90:746
#15  0x417682 in __m_driver_MOD_driver at m_driver.F90:705 (discriminator 2)
#14  0x428A09 in __m_gstateimg_MOD_gstateimg at m_gstateimg.F90:566
#13  0x52B453 in __m_gstate_MOD_gstate at m_gstate.F90:1331
#16  0x40C2EE in MAIN__ at abinit.F90:444
#13  0x52B453 in __m_gstate_MOD_gstate at m_gstate.F90:1331
#15  0x417682 in __m_driver_MOD_driver at m_driver.F90:705 (discriminator 2)
#14  0x428A09 in __m_gstateimg_MOD_gstateimg at m_gstateimg.F90:566
#16  0x40C2EE in MAIN__ at abinit.F90:444
#14  0x428A09 in __m_gstateimg_MOD_gstateimg at m_gstateimg.F90:566
#15  0x417682 in __m_driver_MOD_driver at m_driver.F90:705 (discriminator 2)
#15  0x417682 in __m_driver_MOD_driver at m_driver.F90:705 (discriminator 2)
#16  0x40C2EE in MAIN__ at abinit.F90:444
#16  0x40C2EE in MAIN__ at abinit.F90:444




I am attaching the input file, output file and config.log file.

Please, suggest me the solution for this problem.

Thank you
Shivaprasad
PhD student
IIT Mandi, India.
Attachments
config.log
(640.57 KiB) Downloaded 55 times
Si.in
(765 Bytes) Downloaded 53 times
Si.out
(25.78 KiB) Downloaded 60 times

ebousquet
Posts: 469
Joined: Tue Apr 19, 2011 11:13 am
Location: University of Liege, Belgium

Re: Segmentation fault - invalid memory reference error in abinit-8.10.3 when running ground state calculation

Post by ebousquet » Wed Aug 12, 2020 4:02 pm

Dear Shivaprasad,
Your config.log looks a bit messy with several things that sound to be mixed-up (declared version and really detected version of the compilers, etc).
Could you follow what is described in this post:
viewtopic.php?f=3&t=4463

Sounds like mpiicc, mpiifort, etc should be used and not what you declared in your config file.
Best wishes,
Eric

shivaprasad
Posts: 5
Joined: Fri Aug 07, 2020 8:09 pm

Re: Segmentation fault - invalid memory reference error in abinit-8.10.3 when running ground state calculation

Post by shivaprasad » Wed Aug 12, 2020 10:29 pm

Dear Eric,

Thank you for going through the config.log file and for the link. I used the configuration option given in the link.
At first, I got the error while running configure saying unable to link fftw (not exactly remember the error, some thing like this)which I think for using the with_fft_flavor="dfti".

So, I modified it to with_fft_flavor="fftw3" and used an additional option with_dft_flavor="libxc" since I wanted to use libxc. This time configuration and compilation is successful. Thank you very much for the suggestion.

Now, I tested with the same silicon input file. Calculation is running faster and converged also. But, the abinit program is writing the below lines in the err file:

Code: Select all

libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
I could not figure out what this message is. Is it acceptable?

Also, running make check produced many errors. I am once again attaching the new config.log file for reference.
Attachments
config.log
new config.log file
(663.19 KiB) Downloaded 53 times

User avatar
jbeuken
Posts: 364
Joined: Tue Aug 18, 2009 9:24 pm
Contact:

Re: Segmentation fault - invalid memory reference error in abinit-8.10.3 when running ground state calculation

Post by jbeuken » Wed Aug 19, 2020 10:26 am

Hi,

concerning the config.log, I didn't see anything serious.
most of the errors are expected: the configure tests the existence of a series of libraries, tools, system features...

concerning

Code: Select all

make check
which kind of errors ?

concerning the errors
libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
it's a network problem : driver, configuration,...
i40iw Linux* Driver for Intel(R) Ethernet Connection X722
Intel® Ethernet Network Adapter X722
contact sysadmin... ;)

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

shivaprasad
Posts: 5
Joined: Fri Aug 07, 2020 8:09 pm

Re: Segmentation fault - invalid memory reference error in abinit-8.10.3 when running ground state calculation

Post by shivaprasad » Thu Aug 20, 2020 7:26 am

Dear jbeuken,

Thank you for going through config.log file and the suggestion related to libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ error. I will try to inform the system admin. I hope that this will not affect the numerical results of calculation?

Concerning make check, I was getting below errors related to number of /fast_t* test directories:

Code: Select all

make  check-local
make[3]: Entering directory `/users/home/shiva/tools/abinit-8.10.3/build/tests'
[ -f "runtests.py" ] && ./runtests.py fast -o1 --no-colors --no-logo || ../../tests/runtests.py fast -o1 --no-colors --no-logo --with-pickle=0
Running on n199.cluster.iitmandi.ac.in -- system Linux -- ncpus 40 -- Python 2.7.5 -- runtests.py-0.6.0
Regenerating database...
Test_suite directory already exists. Files will be removed
Running 26 test(s) with MPI_nprocs=1, OMP_nthreads=1, py_nthreads=1...
[TIP] runtests.py is using 1 CPUs but your architecture has 40 CPUs
You may want to use python threads to speed up the execution
Use `runtests -jNUM` to run with NUM threads
Command   /users/home/shiva/tools/abinit-8.10.3/build/src/98_main/abinit < /users/home/shiva/tools/abinit-8.10.3/build/tests/Test_suite/fast_t00/t00.stdin > /users/home/shiva/tools/abinit-8.10.3/build/tests/Test_suite/fast_t00/t00.stdout 2> /users/home/shiva/tools/abinit-8.10.3/build/tests/Test_suite/fast_t00/t00.stderr
 returned exit_code: 24

[fast][t00][np=1]: fldiff.pl fatal error:
Unable to open input file /users/home/shiva/tools/abinit-8.10.3/build/tests/Test_suite/fast_t00/t00.out [file=t00.out]
[fast][t00][np=1]Test was not expected to fail but subprocesses returned 24
forrtl: severe (24): end-of-file during read, unit 5, file /proc/39910/fd/0
Image              PC                Routine            Line        Source             
libifcoremt.so.5   00002B0346BDF7B6  for__io_return        Unknown  Unknown
libifcoremt.so.5   00002B0346C1DC70  for_read_seq_fmt      Unknown  Unknown
abinit             00000000019408B9  Unknown               Unknown  Unknown
abinit             00000000004096B4  Unknown               Unknown  Unknown
abinit             0000000000409382  Unknown               Unknown  Unknown
libc-2.17.so       00002B0349109555  __libc_start_main     Unknown  Unknown
abinit             0000000000409289  Unknown               Unknown  Unknown

And also, related to t*.out files

Code: Select all

/bin/sh: line 0: cd: sources/lapack-abinit_6.10: No such file or directory
make[2]: [check-local] Error 1 (ignored)
/bin/sh: line 0: cd: sources/netcdf-4.1.1: No such file or directory
make[2]: [check-local] Error 1 (ignored)
/bin/sh: line 0: cd: sources/atompaw-4.0.1.0: No such file or directory
make[2]: [check-local] Error 1 (ignored)
/bin/sh: line 0: cd: sources/wannier90-2.0.1.1: No such file or directory
make[2]: [check-local] Error 1 (ignored)
/bin/sh: line 0: cd: sources/etsf_io-1.0.4: No such file or directory
make[2]: [check-local] Error 1 (ignored)
/bin/sh: line 0: cd: sources/bigdft-1.7.1.25: No such file or directory
make[2]: [check-local] Error 1 (ignored)
/users/home/shiva/tools/abinit-8.10.3/tests/pymods/testsuite.py:3344: UserWarning: exception while adding /users/home/shiva/tools/abinit-8.10.3/build/tests/Test_suite/fast_t00/t00.out to tarball:
[Errno 2] No such file or directory: '/users/home/shiva/tools/abinit-8.10.3/build/tests/Test_suite/fast_t00/t00.out'

Thank you once again,
Shivaprasad.

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jbeuken
Posts: 364
Joined: Tue Aug 18, 2009 9:24 pm
Contact:

Re: Segmentation fault - invalid memory reference error in abinit-8.10.3 when running ground state calculation

Post by jbeuken » Wed Aug 26, 2020 12:39 pm

Hi,
make check-local
make[3]: Entering directory `/users/home/shiva/tools/abinit-8.10.3/build/tests'
[ -f "runtests.py" ] && ./runtests.py fast -o1 --no-colors --no-logo || ../../tests/runtests.py fast -o1 --no-colors --no-logo --with-pickle=0
...
[fast][t00][np=1]: fldiff.pl fatal error:
Unable to open input file /users/home/shiva/tools/abinit-8.10.3/build/tests/Test_suite/fast_t00/t00.out [file=t00.out]
[fast][t00][np=1]Test was not expected to fail but subprocesses returned 24
forrtl: severe (24): end-of-file during read, unit 5, file /proc/39910/fd/0
Image PC Routine Line Source
libifcoremt.so.5 00002B0346BDF7B6 for__io_return Unknown Unknown
libifcoremt.so.5 00002B0346C1DC70 for_read_seq_fmt Unknown Unknown
abinit 00000000019408B9 Unknown Unknown Unknown
abinit 00000000004096B4 Unknown Unknown Unknown
abinit 0000000000409382 Unknown Unknown Unknown
libc-2.17.so 00002B0349109555 __libc_start_main Unknown Unknown
abinit 0000000000409289 Unknown Unknown Unknown
This is obviously not normal!

what is the output of these cmds:

Code: Select all

cd /users/home/shiva/tools/abinit-8.10.3/build
ldd src/98_main/abinit
src/98_main/abinit -b
jmb
------
Jean-Michel Beuken
Computer Scientist

shivaprasad
Posts: 5
Joined: Fri Aug 07, 2020 8:09 pm

Re: Segmentation fault - invalid memory reference error in abinit-8.10.3 when running ground state calculation

Post by shivaprasad » Thu Aug 27, 2020 10:51 am

Dear Jbeuken,

Below I am pasting the output of the commands:

1.

Code: Select all

cd /users/home/shiva/tools/abinit-8.10.3/build
ldd src/98_main/abinit
[ linux-vdso.so.1 => (0x00007ffd90b2e000)
libfftw3.so.3 => /lib64/libfftw3.so.3 (0x00002b7b5b849000)
libmkl_intel_lp64.so => /home/shiva/intel/compilers_and_libraries_2019.4.243/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so (0x00002b7b5bbce000)
libmkl_sequential.so => /home/shiva/intel/compilers_and_libraries_2019.4.243/linux/mkl/lib/intel64_lin/libmkl_sequential.so (0x00002b7b5c746000)
libmkl_core.so => /home/shiva/intel/compilers_and_libraries_2019.4.243/linux/mkl/lib/intel64_lin/libmkl_core.so (0x00002b7b5dcdf000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b7b61fb4000)
libm.so.6 => /lib64/libm.so.6 (0x00002b7b621d0000)
librt.so.1 => /lib64/librt.so.1 (0x00002b7b624d2000)
libmpifort.so.12 => /home/shiva/intel/compilers_and_libraries_2019.4.243/linux/mpi/intel64/lib/libmpifort.so.12 (0x00002b7b626da000)
libmpi.so.12 => /home/shiva/intel/compilers_and_libraries_2019.4.243/linux/mpi/intel64/lib/release/libmpi.so.12 (0x00002b7b62a99000)
libdl.so.2 => /lib64/libdl.so.2 (0x00002b7b6398b000)
libifport.so.5 => /home/shiva/intel/compilers_and_libraries_2019.4.243/linux/compiler/lib/intel64_lin/libifport.so.5 (0x00002b7b63b8f000)
libifcoremt.so.5 => /home/shiva/intel/compilers_and_libraries_2019.4.243/linux/compiler/lib/intel64_lin/libifcoremt.so.5 (0x00002b7b63dbd000)
libimf.so => /home/shiva/intel/compilers_and_libraries_2019.4.243/linux/compiler/lib/intel64_lin/libimf.so (0x00002b7b64152000)
libsvml.so => /home/shiva/intel/compilers_and_libraries_2019.4.243/linux/compiler/lib/intel64_lin/libsvml.so (0x00002b7b646f2000)
libirc.so => /home/shiva/intel/compilers_and_libraries_2019.4.243/linux/compiler/lib/intel64_lin/libirc.so (0x00002b7b66096000)
libc.so.6 => /lib64/libc.so.6 (0x00002b7b66308000)
/lib64/ld-linux-x86-64.so.2 (0x00002b7b5b625000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b7b666d6000)
libfabric.so.1 => /home/shiva/intel/compilers_and_libraries_2019.4.243/linux/mpi/intel64/libfabric/lib/libfabric.so.1 (0x00002b7b668ec000)
libintlc.so.5 => /home/shiva/intel/compilers_and_libraries_2019.4.243/linux/compiler/lib/intel64_lin/libintlc.so.5 (0x00002b7b66b24000)/quote]

2.

Code: Select all

src/98_main/abinit -b
DATA TYPE INFORMATION:
REAL: Data type name: REAL(DP)
Kind value: 8
Precision: 15
Smallest nonnegligible quantity relative to 1: 0.22204460E-15
Smallest positive number: 0.22250739-307
Largest representable number: 0.17976931+309
INTEGER: Data type name: INTEGER(default)
Kind value: 4
Bit size: 32
Largest representable number: 2147483647
LOGICAL: Data type name: LOGICAL
Kind value: 4
CHARACTER: Data type name: CHARACTER Kind value: 1
==== Using MPI-2 specifications ====
MPI-IO support is ON
xmpi_tag_ub ................ 1073741823
xmpi_bsize_ch .............. 1
xmpi_bsize_int ............. 4
xmpi_bsize_sp .............. 4
xmpi_bsize_dp .............. 8
xmpi_bsize_spc ............. 8
xmpi_bsize_dpc ............. 16
xmpio_bsize_frm ............ 4
xmpi_address_kind .......... 8
xmpi_offset_kind ........... 8
MPI_WTICK .................. 4.166667057021160E-010

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
CPP options activated during the build:

CC_INTEL CXX_GNU FC_INTEL

HAVE_FC_ALLOCATABLE_DT... HAVE_FC_ASYNC HAVE_FC_COMMAND_ARGUMENT

HAVE_FC_COMMAND_LINE HAVE_FC_CONTIGUOUS HAVE_FC_CPUTIME

HAVE_FC_EXIT HAVE_FC_FLUSH HAVE_FC_GAMMA

HAVE_FC_IEEE_EXCEPTIONS HAVE_FC_IOMSG HAVE_FC_ISO_C_BINDING

HAVE_FC_ISO_FORTRAN_2008 HAVE_FC_LONG_LINES HAVE_FC_MOVE_ALLOC

HAVE_FC_PRIVATE HAVE_FC_PROTECTED HAVE_FC_STREAM_IO

HAVE_FFT HAVE_FFT_FFTW3 HAVE_FFT_MPI

HAVE_FFT_SERIAL HAVE_GW_DPC HAVE_LIBPAW_ABINIT

HAVE_LIBTETRA_ABINIT HAVE_LIBXC HAVE_LINALG

HAVE_LINALG_SERIAL HAVE_MPI HAVE_MPI2

HAVE_MPI_IALLREDUCE HAVE_MPI_IALLTOALL HAVE_MPI_IALLTOALLV

HAVE_MPI_INTEGER16 HAVE_MPI_IO HAVE_MPI_TYPE_CREATE_S...

HAVE_NUMPY HAVE_OS_LINUX HAVE_TIMER_ABINIT

USE_MACROAVE
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

=== Build Information ===
Version : 8.10.3
Build target : x86_64_linux_intel19.0
Build date : 20200812

=== Compiler Suite ===
C compiler : intel19.0
C++ compiler : gnu19.0
Fortran compiler : intel19.0
CFLAGS : -g -O3 -vec-report0
CXXFLAGS : -m64 -g -O3 -mtune=native -march=native
FCFLAGS : -g -extend-source -vec-report0 -noaltparam -nofpscomp
FC_LDFLAGS : -static-intel -static-libgcc

=== Optimizations ===
Debug level : basic
Optimization level : aggressive
Architecture : intel_xeon

=== 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
FFT flavor : fftw3
LINALG flavor : mkl
MATH flavor : none
TIMER flavor : abinit
TRIO flavor : none

=== Experimental features ===
Bindings : @enable_bindings@
Exports : no
GW double-precision : yes

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Default optimizations:
-O3 -xHOST


Optimizations for 43_ptgroups:
-O0


++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
What is the error that is occurring? Am I doing any mistake in compiling ?

Thank you,
Shivaprasad.

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gmatteo
Posts: 291
Joined: Sun Aug 16, 2009 5:40 pm

Re: Segmentation fault - invalid memory reference error in abinit-8.10.3 when running ground state calculation

Post by gmatteo » Tue Sep 08, 2020 10:11 pm

Avoid mixing FFTW3 with MKL as MKL provides wrappers for fftw3 calling the intel DFTI FFT library.
This means that the linker will receive multiple definitions for the same procedure and
results are unpredictable!
Either use MKL for linalg and fft or FFTW3 with e.g. openblas for linalg.

shivaprasad
Posts: 5
Joined: Fri Aug 07, 2020 8:09 pm

Re: Segmentation fault - invalid memory reference error in abinit-8.10.3 when running ground state calculation

Post by shivaprasad » Thu Sep 24, 2020 6:15 am

Thank you gmatteo for your suggestion. I will try with the options you have told and check.

Thank you,
Shivaprasad

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