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Error occured during mst2 run: forrtl: severe (174): SIGSEGV, segmentation fault occurred #28

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KylinGuo opened this issue Nov 28, 2022 · 11 comments
Closed

Error occured during mst2 run: forrtl: severe (174): SIGSEGV, segmentation fault occurred #28

KylinGuo opened this issue Nov 28, 2022 · 11 comments

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@KylinGuo
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KylinGuo commented Nov 28, 2022 •
edited
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I just compile MuST code by running the two commands:
(1) make linux-intel-nogpu
(2) make install
Note:
(1) No changes in "MuST-1.8.3.6/architecture/linux-intel-nogpu"
(2) parallel studio xe 2018.4.057 is used.

An Error occured during mst2 run. I am runing the example located at MuST/Tutorials/CuZn/B2. Here are the details.
== Beigin ==

$ mpirun -np 2 ~/softwares/MuST-1.8.3.6/bin/mst2 < i_new 
  
             ********************************************************
             *                                                      *
             *              Fortran 90 Interface Module             *
             *                                                      *
             *                         For                          *
             *                                                      *
             *              MPI Message Passing Library             *
             *                                                      *
             *                   Version No. 2.0k                   *
             *                                                      *
             ********************************************************
  
 CHARACTER_BYTES =            1
 INTEGER_BYTES   =            4
 REAL_BYTES      =            8
 COMPLEX_BYTES   =           16
 ADDRESS_BYTES   =            8
  
 Number of Procs =            2
  
Execution starts at 12:45:34, 11-28-2022 on     2 nodes
#-------------------------------------------------------------------------------
#
#
#           ********************************************************
#           *                                                      *
#           *    Full-Potential Multiple Scattering Theory Based   *
#           *                                                      *
#           *  Ab Initio Electronic Structure Calculation Package  *
#           *                                                      *
#           ********************************************************
#
#
#   username                 : guoqilin
#   system name              : slurm-login-2
#   code compiled            : Monday, November 28 2022 10:22:54
#   MuST source code version : Develop
#-------------------------------------------------------------------------------

 The Position Data File: ./position.dat

 The Position Data is read successfully!


================================================================================

 The lattice system is: Cubic       

********************************
* Output from SPACEGRP         *
********************************

The point group of the crystal is the full cubic        group
Space group is symmorphic
--------------------------------------------------------------------------------

********************************
* Output from CHECKSYMM        *
********************************

Symmetry is correct
--------------------------------------------------------------------------------

********************************
* Output from SPACEGRP         *
********************************

The point group of the crystal is the full cubic        group
Space group is symmorphic
--------------------------------------------------------------------------------

********************************
* Output from SPKPT            *
********************************

Timing in setting up wvkl:     0     0.10800
Wavevector mesh contains    1728 points
--------------------------------------------------------------------------------

================================================================================

            *********************************************
            *     Output from createParallelization     *
            *            in ProcMappingModule           *
            *********************************************

The number of processors in each box :    2
The number of repeats along k-dimen. :    1
The number of repeats along e-dimen. :    1
Dimension of the box (to be repeated to produce processor grid):    2  X    1  X    1
Dimension of processors :    2  X    1  X    1
Proc Grid Dimension:      3
Total Number of Procs:    2
Proc Grid Size in Each Dimension: (  2,  1,  1)
MyPE =     0 is at (  0,  0,  0)
MyPE =     1 is at (  1,  0,  0)
MyPE =     0, NumEs, NumEsPerBox =    30   30
MyPE =     1, NumEs, NumEsPerBox =    30   30
MyPE =     1, NumKs, NumKsPerBox =    56   56
MyPE =     1, K index =     1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16, ...,...
Energy point index =     1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20, ...
Process in E-group =     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0, ...
MyPE =     0, NumKs, NumKsPerBox =    56   56
MyPE =     0, K index =     1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16, ...,...
IBZ K point index  =     1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20, ...,...
Process in K-group =     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0, ...,...

================================================================================

The number of processes that write output data:      1
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source             
libifcore.so.5     00007F57F9FAE9AC  for__signal_handl     Unknown  Unknown
libpthread-2.17.s  00007F57F8908630  Unknown               Unknown  Unknown
mst2               0000000000726DE0  Unknown               Unknown  Unknown
mst2               000000000040E883  Unknown               Unknown  Unknown
mst2               000000000040925E  Unknown               Unknown  Unknown
libc-2.17.so       00007F57F824B555  __libc_start_main     Unknown  Unknown
mst2               0000000000409169  Unknown               Unknown  Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source             
libifcore.so.5     00007FC890D4C9AC  for__signal_handl     Unknown  Unknown
libpthread-2.17.s  00007FC88F6A6630  Unknown               Unknown  Unknown
mst2               0000000000726DE0  Unknown               Unknown  Unknown
mst2               000000000040E883  Unknown               Unknown  Unknown
mst2               000000000040925E  Unknown               Unknown  Unknown
libc-2.17.so       00007FC88EFE9555  __libc_start_main     Unknown  Unknown
mst2               0000000000409169  Unknown               Unknown  Unknown

== End ==
@wangy2014
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How did you install the code? Which compiler and MPI library are you using? If your job produced an o_n000000_CuZn file, what is the last message saying in the file?

@wangy2014
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The compiler you are using is a bit old. To find out what is causing the problem, you may edit architectures/linux-intel-nogpu file and set "FFLAGS = -I. -O3 -CB -CU -traceback -ftrapuv -fpe0 -ftz -fp-stack-check". After you finish the change, type "make clean" to delete all the binary files produced in the previous compilation. Once this is done, you can rebuild the code by executing "make linux-intel-nogpu" and then "make install". After the code is recompiled, you may run the test again. The job will crash, but will give you detailed information on what part of the code is causing the crash. One I know the information, I might be able to tell how to avoid or fix the problem.

@KylinGuo
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Dear Wang, I plan to use intel fortran compiler, Intel MKL and Intel MPI, so I first load the Intel environment via source /hpc/software/intel/ps2018/parallel_studio_xe_2018.4.057/bin/psxevars.sh intel64, and It says

$ source /hpc/software/intel/ps2018/parallel_studio_xe_2018.4.057/bin/psxevars.sh intel64
Intel(R) Parallel Studio XE 2018 Update 4 for Linux*
Copyright (C) 2009-2018 Intel Corporation. All rights reserved.
$ ifort -V
Intel(R) Fortran Intel(R) 64 Compiler for applications running on Intel(R) 64, Version 18.0.5.274 Build 20180823
Copyright (C) 1985-2018 Intel Corporation.  All rights reserved.
$ mpiifort -V
Intel(R) Fortran Intel(R) 64 Compiler for applications running on Intel(R) 64, Version 18.0.5.274 Build 20180823
Copyright (C) 1985-2018 Intel Corporation.  All rights reserved.
$ mpirun -V
Intel(R) MPI Library for Linux* OS, Version 2018 Update 4 Build 20180823 (id: 18555)
Copyright 2003-2018 Intel Corporation.

And then I run the following commands to build the code

$ make linux-intel-nogpu
$ make install

@KylinGuo
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The compiler you are using is a bit old. To find out what is causing the problem, you may edit architectures/linux-intel-nogpu file and set "FFLAGS = -I. -O3 -CB -CU -traceback -ftrapuv -fpe0 -ftz -fp-stack-check". After you finish the change, type "make clean" to delete all the binary files produced in the previous compilation. Once this is done, you can rebuild the code by executing "make linux-intel-nogpu" and then "make install". After the code is recompiled, you may run the test again. The job will crash, but will give you detailed information on what part of the code is causing the crash. One I know the information, I might be able to tell how to avoid or fix the problem.

Dear Wang, I plan to use intel fortran compiler, Intel MKL and Intel MPI, so I first load the Intel environment via source /hpc/software/intel/ps2018/parallel_studio_xe_2018.4.057/bin/psxevars.sh intel64, and It says

$ source /hpc/software/intel/ps2018/parallel_studio_xe_2018.4.057/bin/psxevars.sh intel64
Intel(R) Parallel Studio XE 2018 Update 4 for Linux*
Copyright (C) 2009-2018 Intel Corporation. All rights reserved.
$ ifort -V
Intel(R) Fortran Intel(R) 64 Compiler for applications running on Intel(R) 64, Version 18.0.5.274 Build 20180823
Copyright (C) 1985-2018 Intel Corporation.  All rights reserved.
$ mpiifort -V
Intel(R) Fortran Intel(R) 64 Compiler for applications running on Intel(R) 64, Version 18.0.5.274 Build 20180823
Copyright (C) 1985-2018 Intel Corporation.  All rights reserved.
$ mpirun -V
Intel(R) MPI Library for Linux* OS, Version 2018 Update 4 Build 20180823 (id: 18555)
Copyright 2003-2018 Intel Corporation.

And then I run the following commands to build the code

$ make linux-intel-nogpu
$ make install

@KylinGuo
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KylinGuo commented Nov 29, 2022 •
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Dear Wang, thank you! I will try this and I am looking forward to use MuST.
I am not familiar with markdown. so I am sorry for the previous dirty page.

@KylinGuo
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The compiler you are using is a bit old. To find out what is causing the problem, you may edit architectures/linux-intel-nogpu file and set "FFLAGS = -I. -O3 -CB -CU -traceback -ftrapuv -fpe0 -ftz -fp-stack-check". After you finish the change, type "make clean" to delete all the binary files produced in the previous compilation. Once this is done, you can rebuild the code by executing "make linux-intel-nogpu" and then "make install". After the code is recompiled, you may run the test again. The job will crash, but will give you detailed information on what part of the code is causing the crash. One I know the information, I might be able to tell how to avoid or fix the problem.

Dear Wang, I recompiled the code in the way as you said. The k_n00000_CuZn file is empty. The stdout is given below.

$ pwd
/home/USERNAME/MuST_WORK/CuZn/B2
$ mpirun -np 2 ~/softwares/MuST-1.8.3.6-ps2018/bin/mst2 < i_new 
  
             ********************************************************
             *                                                      *
             *              Fortran 90 Interface Module             *
             *                                                      *
             *                         For                          *
             *                                                      *
             *              MPI Message Passing Library             *
             *                                                      *
             *                   Version No. 2.0k                   *
             *                                                      *
             ********************************************************
  
 CHARACTER_BYTES =            1
 INTEGER_BYTES   =            4
 REAL_BYTES      =            8
 COMPLEX_BYTES   =           16
 ADDRESS_BYTES   =            8
  
 Number of Procs =            2
  
Execution starts at 00:38:45, 11-30-2022 on     2 nodes
#-------------------------------------------------------------------------------
#
#
#           ********************************************************
#           *                                                      *
#           *    Full-Potential Multiple Scattering Theory Based   *
#           *                                                      *
#           *  Ab Initio Electronic Structure Calculation Package  *
#           *                                                      *
#           ********************************************************
#
#
#   username                 : USERNAME
#   system name              : slurm-login-2
#   code compiled            : Tuesday, November 29 2022 15:26:25
#   MuST source code version : Develop
#-------------------------------------------------------------------------------

 The Position Data File: ./position.dat

 The Position Data is read successfully!


================================================================================

 The lattice system is: Cubic       

********************************
* Output from SPACEGRP         *
********************************

The point group of the crystal is the full cubic        group
Space group is symmorphic
--------------------------------------------------------------------------------

********************************
* Output from CHECKSYMM        *
********************************

Symmetry is correct
--------------------------------------------------------------------------------

********************************
* Output from SPACEGRP         *
********************************

The point group of the crystal is the full cubic        group
Space group is symmorphic
--------------------------------------------------------------------------------

********************************
* Output from SPKPT            *
********************************

Timing in setting up wvkl:     0     0.26400
Wavevector mesh contains    1728 points
--------------------------------------------------------------------------------

================================================================================

            *********************************************
            *     Output from createParallelization     *
            *            in ProcMappingModule           *
            *********************************************

The number of processors in each box :    2
The number of repeats along k-dimen. :    1
The number of repeats along e-dimen. :    1
Dimension of the box (to be repeated to produce processor grid):    2  X    1  X    1
Dimension of processors :    2  X    1  X    1
Proc Grid Dimension:      3
Total Number of Procs:    2
Proc Grid Size in Each Dimension: (  2,  1,  1)
MyPE =     0 is at (  0,  0,  0)
MyPE =     1 is at (  1,  0,  0)
MyPE =     0, NumEs, NumEsPerBox =    30   30
MyPE =     1, NumEs, NumEsPerBox =    30   30
MyPE =     1, NumKs, NumKsPerBox =    56   56
MyPE =     1, K index =     1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16, ...,...
Energy point index =     1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20, ...
Process in E-group =     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0, ...
MyPE =     0, NumKs, NumKsPerBox =    56   56
MyPE =     0, K index =     1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16, ...,...
IBZ K point index  =     1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20, ...,...
Process in K-group =     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0, ...,...

================================================================================

The number of processes that write output data:      1
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source             
libifcore.so.5     00007F682C19D9AC  for__signal_handl     Unknown  Unknown
libpthread-2.17.s  00007F682AAF7630  Unknown               Unknown  Unknown
mst2               0000000000D7EF01  corestatesmodule_        5107  CoreStatesModule.F90
mst2               0000000000D6384F  corestatesmodule_        1903  CoreStatesModule.F90
mst2               0000000000416724  MAIN__                   1557  mst2.F90
mst2               0000000000408ADE  Unknown               Unknown  Unknown
libc-2.17.so       00007F682A43A555  __libc_start_main     Unknown  Unknown
mst2               00000000004089E9  Unknown               Unknown  Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source             
libifcore.so.5     00007F28B08C59AC  for__signal_handl     Unknown  Unknown
libpthread-2.17.s  00007F28AF21F630  Unknown               Unknown  Unknown
mst2               0000000000D7EF01  corestatesmodule_        5107  CoreStatesModule.F90
mst2               0000000000D6384F  corestatesmodule_        1903  CoreStatesModule.F90
mst2               0000000000416724  MAIN__                   1557  mst2.F90
mst2               0000000000408ADE  Unknown               Unknown  Unknown
libc-2.17.so       00007F28AEB62555  __libc_start_main     Unknown  Unknown
mst2               00000000004089E9  Unknown               Unknown  Unknown

@wangy2014
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Is there o_n000000_CuZn file generated? If so, what is the message in the file?
I am also surprised that the standard output does not show any useful information even though you have set FFLAGS as I told you. Would you show me your new linux-intel-nogpu?

@wangy2014 wangy2014 reopened this Nov 30, 2022
@KylinGuo
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o_n000000_CuZn

Dear Wang, the o_n00000_CuZn file is generated. Here is the message in this file.

 $ cat o_n00000_CuZn 
Current working directory: /home/guoqilin/MuST_WORK/CuZn/B2
Execution command: /home/guoqilin/softwares/MuST-1.8.3.6-ps2018/bin/mst2
Execution starts at 00:38:45, 11-30-2022 on     2 nodes of slurm-login-2
#-------------------------------------------------------------------------------
#
#
#           ********************************************************
#           *                                                      *
#           *    Full-Potential Multiple Scattering Theory Based   *
#           *                                                      *
#           *  Ab Initio Electronic Structure Calculation Package  *
#           *                                                      *
#           ********************************************************
#
#
#   username                 : guoqilin
#   system name              : slurm-login-2
#   code compiled            : Tuesday, November 29 2022 15:26:25
#   MuST source code version : Develop
#-------------------------------------------------------------------------------
            Number of atoms on each processor:                  1
            Number of k-points on each processor:              56
            Number of redundant k-points on each processor:     0
            Number of energies on each processor:              30
            Number of redundant energies on each processor:     0

================================================================================

--------------------------------------------------------------------------------

                          *****************************
                          * Output from print_threads *
                          *****************************

                      code is compiled without using threads

================================================================================

              ::::  KKR Electronic Structure Calculation ::::


--------------------------------------------------------------------------------

                     **************************************
                     *   Output from printPotentialType   *
                     **************************************


================================================================================
# Potential Type          : Muffin-Tin

================================================================================

--------------------------------------------------------------------------------

                        ********************************
                        *   Output from printScfData   *
                        ********************************


================================================================================
# Single Site Solver: Spherical
# MST Method        : KKR
# Spin Parameter    : Non-magnetic -  1
================================================================================

--------------------------------------------------------------------------------

                        *******************************
                        *   Output from printSystem   *
                        *******************************


================================================================================
# Number of Atoms         :      2
# Bravais Lattice Vector  :
#         5.53000000   0.00000000   0.00000000
#         0.00000000   5.53000000   0.00000000
#         0.00000000   0.00000000   5.53000000
================================================================================

--------------------------------------------------------------------------------

                           *************************
                           * Output from printAtom *
                           *************************

================================================================================
Atom Name       : Cu
Input  Potential: ./Cu_mt_v                                         
Output Potential: ./CuZn_mt_w                                       
Global Index    :      1
Atom Position   :    0.00000   0.00000   0.00000
Local Moment    :    0.00000
Local evec_old  :    0.00000   0.00000   1.00000
Constrain Fld   :    0.00000   0.00000   0.00000
Potential Mixing Parameter:  0.10000
Density   Mixing Parameter:  0.10000
Charge    Mixing Parameter:  1.00000
Moment    Mixing Parameter:  0.10000
Evec      Mixing Algorithm:  0.00000
Number of Shells in LIZ:   16
Lmax for each LIZ shell:    3   3   3   3   3   3   3   3   3   3
Lmax for each LIZ shell:    3   3   3   3   3   3
Number of r-mesh less or equal than Rmt:  1001
Ratio of r-mesh steps, hin and hout    :     1
exponential step of inside r-mesh   :   0.010000
Desired Rmt         :    2.39456
Desired Core Radius :    2.39456
================================================================================
 setupLIZ :: Number of cell shifts:         343
                             nXmax:           3           3           3
                             nXmin:          -3          -3          -3

--------------------------------------------------------------------------------

                          *****************************
                          * Output from printNeighbor *
                          *****************************


================================================================================
 Local Atom Index =     1
 Number of neighboring atoms in LIZ =    26
 Neighboring Atom List:
 ============================================================================
   Z    Lmax    Proc   L-Index     G-Index shell            Position
 ----------------------------------------------------------------------------
  30      3        1         1        2      1   -2.76500  -2.76500  -2.76500
  30      3        1         1        2      1    2.76500  -2.76500  -2.76500
  30      3        1         1        2      1   -2.76500   2.76500  -2.76500
  30      3        1         1        2      1    2.76500   2.76500  -2.76500
  30      3        1         1        2      1   -2.76500  -2.76500   2.76500
  30      3        1         1        2      1    2.76500  -2.76500   2.76500
  30      3        1         1        2      1   -2.76500   2.76500   2.76500
  30      3        1         1        2      1    2.76500   2.76500   2.76500
  29      3        0         1        1      2    0.00000   0.00000  -5.53000
  29      3        0         1        1      2    0.00000  -5.53000   0.00000
  29      3        0         1        1      2   -5.53000   0.00000   0.00000
  29      3        0         1        1      2    5.53000   0.00000   0.00000
  29      3        0         1        1      2    0.00000   5.53000   0.00000
  29      3        0         1        1      2    0.00000   0.00000   5.53000
  29      3        0         1        1      3    0.00000  -5.53000  -5.53000
  29      3        0         1        1      3   -5.53000   0.00000  -5.53000
  29      3        0         1        1      3    5.53000   0.00000  -5.53000
  29      3        0         1        1      3    0.00000   5.53000  -5.53000
  29      3        0         1        1      3   -5.53000  -5.53000   0.00000
  29      3        0         1        1      3    5.53000  -5.53000   0.00000
  29      3        0         1        1      3   -5.53000   5.53000   0.00000
  29      3        0         1        1      3    5.53000   5.53000   0.00000
  29      3        0         1        1      3    0.00000  -5.53000   5.53000
  29      3        0         1        1      3   -5.53000   0.00000   5.53000
  29      3        0         1        1      3    5.53000   0.00000   5.53000
  29      3        0         1        1      3    0.00000   5.53000   5.53000
 ============================================================================
 Number of shells:     3
 shell   1:   radius:     4.78912     atoms:     8
 shell   2:   radius:     5.53000     atoms:     6
 shell   3:   radius:     7.82060     atoms:    12
 ============================================================================

  Send Table of Process #       0
  ==============================================
  Local Atom     Num Clients      Client Process
  ----------------------------------------------
       1               1                   1
      ------------------------------------------
      Num of Requests from Remote Atoms:    1
      ------------------------------------------
  ==============================================

  Receive Table of Process #       0
  ==============================================
  Local Atom     Num Servers      Server Process
  ----------------------------------------------
       1               1                   1
      ------------------------------------------
      Num of Requests upon Remote Atoms:    8
      ------------------------------------------
  ==============================================

*******************************
* Output from printBZone      *
*******************************

Number of K Meshes =     1

=================================================
Mesh index         =     1
Number of K points =    56
=================================================
     kx           ky           kz           wght 
-------------------------------------------------
   0.08288      0.08288      0.08288      8.00000
   0.08288      0.08288      0.06781     24.00000
   0.08288      0.08288      0.05274     24.00000
   0.08288      0.08288      0.03767     24.00000
   0.08288      0.08288      0.02260     24.00000
   0.08288      0.08288      0.00753     24.00000
   0.08288      0.06781      0.06781     24.00000
   0.08288      0.06781      0.05274     48.00000
   0.08288      0.06781      0.03767     48.00000
   0.08288      0.06781      0.02260     48.00000
   0.08288      0.06781      0.00753     48.00000
   0.08288      0.05274      0.05274     24.00000
   0.08288      0.05274      0.03767     48.00000
   0.08288      0.05274      0.02260     48.00000
   0.08288      0.05274      0.00753     48.00000
   0.08288      0.03767      0.03767     24.00000
   0.08288      0.03767      0.02260     48.00000
   0.08288      0.03767      0.00753     48.00000
   0.08288      0.02260      0.02260     24.00000
   0.08288      0.02260      0.00753     48.00000
   0.08288      0.00753      0.00753     24.00000
   0.06781      0.06781      0.06781      8.00000
   0.06781      0.06781      0.05274     24.00000
   0.06781      0.06781      0.03767     24.00000
   0.06781      0.06781      0.02260     24.00000
   0.06781      0.06781      0.00753     24.00000
   0.06781      0.05274      0.05274     24.00000
   0.06781      0.05274      0.03767     48.00000
   0.06781      0.05274      0.02260     48.00000
   0.06781      0.05274      0.00753     48.00000
   0.06781      0.03767      0.03767     24.00000
   0.06781      0.03767      0.02260     48.00000
   0.06781      0.03767      0.00753     48.00000
   0.06781      0.02260      0.02260     24.00000
   0.06781      0.02260      0.00753     48.00000
   0.06781      0.00753      0.00753     24.00000
   0.05274      0.05274      0.05274      8.00000
   0.05274      0.05274      0.03767     24.00000
   0.05274      0.05274      0.02260     24.00000
   0.05274      0.05274      0.00753     24.00000
   0.05274      0.03767      0.03767     24.00000
   0.05274      0.03767      0.02260     48.00000
   0.05274      0.03767      0.00753     48.00000
   0.05274      0.02260      0.02260     24.00000
   0.05274      0.02260      0.00753     48.00000
   0.05274      0.00753      0.00753     24.00000
   0.03767      0.03767      0.03767      8.00000
   0.03767      0.03767      0.02260     24.00000
   0.03767      0.03767      0.00753     24.00000
   0.03767      0.02260      0.02260     24.00000
   0.03767      0.02260      0.00753     48.00000
   0.03767      0.00753      0.00753     24.00000
   0.02260      0.02260      0.02260      8.00000
   0.02260      0.02260      0.00753     24.00000
   0.02260      0.00753      0.00753     24.00000
   0.00753      0.00753      0.00753      8.00000
=================================================

--------------------------------------------------------------------------------

                        *********************************
                        *  Output from printPolyhedron  *
                        *********************************

Atom index:                     1
Number of boundary planes:     14
Number of corners:             24
Number of edges:               48
Cell volume:                  84.55619
Cell surface area:           102.38718
Inscribed sphere radius:       2.39456
Wigner-Seitz sphere radius:    2.72282
Bounding sphere radius:        3.09136

Plane Table
================================================================================
Plane  Nb Atom  No Corners          Plane Vector            Distance      Area
--------------------------------------------------------------------------------
  1       2          6      -1.38250   1.38250  -1.38250     2.39456     9.93144
  2       2          6       1.38250  -1.38250  -1.38250     2.39456     9.93144
  3       2          6      -1.38250  -1.38250   1.38250     2.39456     9.93144
  4       2          6       1.38250   1.38250  -1.38250     2.39456     9.93144
  5       2          6       1.38250  -1.38250   1.38250     2.39456     9.93144
  6       2          6      -1.38250  -1.38250  -1.38250     2.39456     9.93144
  7       2          6       1.38250   1.38250   1.38250     2.39456     9.93144
  8       2          6      -1.38250   1.38250   1.38250     2.39456     9.93144
  9       1          4       2.76500   0.00000   0.00000     2.76500     3.82261
 10       1          4       0.00000   2.76500   0.00000     2.76500     3.82261
 11       1          4       0.00000   0.00000   2.76500     2.76500     3.82261
 12       1          4       0.00000   0.00000  -2.76500     2.76500     3.82261
 13       1          4       0.00000  -2.76500   0.00000     2.76500     3.82261
 14       1          4      -2.76500   0.00000   0.00000     2.76500     3.82261
================================================================================

Corner Table
================================================================================
Corner             Corner Vector             Corner Distance
--------------------------------------------------------------------------------
   1         0.00000   1.38250  -2.76500          3.09136
   2        -1.38250   0.00000  -2.76500          3.09136
   3        -2.76500   0.00000  -1.38250          3.09136
   4        -1.38250   2.76500   0.00000          3.09136
   5        -2.76500   1.38250   0.00000          3.09136
   6         2.76500   0.00000  -1.38250          3.09136
   7         1.38250   0.00000  -2.76500          3.09136
   8         2.76500  -1.38250   0.00000          3.09136
   9         1.38250  -2.76500   0.00000          3.09136
  10         0.00000  -1.38250  -2.76500          3.09136
  11         0.00000  -2.76500  -1.38250          3.09136
  12         0.00000  -1.38250   2.76500          3.09136
  13         0.00000  -2.76500   1.38250          3.09136
  14        -1.38250  -2.76500   0.00000          3.09136
  15        -2.76500  -1.38250   0.00000          3.09136
  16        -1.38250   0.00000   2.76500          3.09136
  17        -2.76500   0.00000   1.38250          3.09136
  18         2.76500   1.38250   0.00000          3.09136
  19         1.38250   2.76500   0.00000          3.09136
  20         2.76500   0.00000   1.38250          3.09136
  21         1.38250   0.00000   2.76500          3.09136
  22         0.00000   2.76500   1.38250          3.09136
  23         0.00000   1.38250   2.76500          3.09136
  24         0.00000   2.76500  -1.38250          3.09136
================================================================================

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------

                         *******************************
                         * Output from printRadialGrid *
                         *******************************

============================================================
Local atom index                       =    1
jmt                                    = 1001
jinsc                                  = 1001
jend                                   = 1027
jend_plus_n                            = 1038
hin                                    = 0.1000000000000D-01
hout                                   = 0.1000000000000D-01
nmult                                  =    1
xstart                                 =-0.9126800401252D+01
xmt                                    = 0.8731995987484D+00
xend                                   = 0.1133199598748D+01
rstart                                 = 0.1087128667745D-03
rmt                                    = 0.2394560241464D+01
rend                                   = 0.3105577221488D+01
4pi/3*rmt^3                            = 0.5751298535376D+02
============================================================

--------------------------------------------------------------------------------

                        *************************************
                        *   Output from printSystemVolume   *
                        *************************************


================================================================================
Total System Volume:                   169.11237700
Total Voronoi Polyhedra Volume:        169.11237700
Total Inscribed Sphere Volume :        115.02597071
Total Muffintin Sphere Volume :        115.02597071
Total Interstitial Volume     :         54.08640629
================================================================================

--------------------------------------------------------------------------------

                        *********************************
                        * Output from printStepFunction *
                        *********************************

Polyhedron Index:                     1
Lmax for the Step Function:          12
Number of Critical Points:            4
Number of Radial Gaussian Points:    57
Number of Theta  Gaussian Points:    60
Inner Bounding Sphere Radius:     2.39456
Outer Bounding Sphere Radius:     3.09136

Non-zero (l,m) components of the step function
( 0, 0), ( 4, 0), ( 4, 4), ( 6, 0), ( 6, 4), ( 8, 0), ( 8, 4), ( 8, 8), (10, 0), (10, 4),
(10, 8), (12, 0), (12, 4), (12, 8), (12,12) 

========================================
Critical Radial Point Table
========================================
Critical R Point         Radius
----------------------------------------
        1                2.39456
        2                2.76500
        3                2.93273
        4                3.09136
========================================

--------------------------------------------------------------------------------

                       **********************************
                       *  Output from testStepFunction  *
                       **********************************

Polyhedron Index:           1
Exact Cell Volume:          0.845561885000D+02
Calculated Cell Volume:     0.845561876655D+02
================================================================================

 Real Space Lattice:: nm1,nm2,nm3   =     4    4    4
                      Rs cut radius =    7.57154
                      Number of Rs  =   729

 Reciprocal Lattice:: nm1,nm2,nm3   =     4    4    4
                      Kn cut radius =   39.83243
                      Number of Kn  =   729

Time:: initMadelung:    0.05100


----------------------------------------------------------
                         *******************************
                         *        PrintMadelung        *
                         *******************************


 Sum over j of Madelung Matrix(j,i) for atom     1:  -0.6580892313759D+00
----------------------------------------------------------

calSymmetryFlags::   Flags, StepFunction

   l   m flag          Re[stepf]                  Im[stepf]        
   0   0   1    0.35415012990726D+01    0.00000000000000D+00
   4   0   1    0.10072660263846D+01    0.00000000000000D+00
   4   4   1    0.60195659024742D+00    0.77365258616287D-14
   6   0   1   -0.33384058415802D+00    0.00000000000000D+00
   6   4   1    0.62455854745275D+00    0.80625588598112D-14
   8   0   1   -0.19403328460140D+00    0.00000000000000D+00
   8   4   1   -0.72966347229751D-01   -0.95586553414577D-15
   8   8   1   -0.11117325715867D+00   -0.27890730547029D-14
  10   0   1   -0.36291792610512D+00    0.00000000000000D+00
  10   4   1    0.36569897667551D+00    0.47387873357739D-14
  10   8   1    0.43526881704269D+00    0.11300326363166D-13
  12   0   1   -0.20205111674178D+00    0.00000000000000D+00
  12   4   1    0.12854290332959D+00    0.16778746398440D-14
  12   8   1    0.20834467440793D+00    0.53634746525697D-14
  12  12   1   -0.11495327699295D+00   -0.45172428606072D-14
------------------------------------------------------------


calSymmetryFlags::   Flags, q_Value

   l   m flag          Re[ql]                     Im[ql]           
   0   0   3   -0.19229603256018D+02    0.00000000000000D+00
------------------------------------------------------------


The crystal system has the point group symmetry!


--------------------------------------------------------------------------------

                       **************************************
                       * Output from printIBZRotationMatrix *
                       **************************************

The lattice system is Cubic       

Number of Rotations =    48
Rotation Matrix = 
================================================================================

      [ 1.00  0.00  0.00]        [ 0.00 -1.00  0.00]        [-1.00 -0.00  0.00]
r( 1)=[ 0.00  1.00  0.00], r( 2)=[ 1.00  0.00  0.00], r( 3)=[ 0.00 -1.00  0.00]
      [ 0.00  0.00  1.00]        [ 0.00  0.00  1.00]        [ 0.00  0.00  1.00]

      [-0.00  1.00  0.00]        [ 0.00  0.00  1.00]        [-1.00  0.00  0.00]
r( 4)=[-1.00 -0.00  0.00], r( 5)=[ 0.00  1.00  0.00], r( 6)=[ 0.00  1.00  0.00]
      [ 0.00  0.00  1.00]        [-1.00  0.00  0.00]        [-0.00  0.00 -1.00]

      [-0.00  0.00 -1.00]        [ 0.00 -1.00  0.00]        [-1.00 -0.00  0.00]
r( 7)=[ 0.00  1.00  0.00], r( 8)=[ 0.00  0.00  1.00], r( 9)=[ 0.00 -0.00  1.00]
      [ 1.00  0.00 -0.00]        [-1.00  0.00  0.00]        [-0.00  1.00  0.00]

      [-0.00  1.00  0.00]        [ 1.00  0.00  0.00]        [-0.00 -0.00 -1.00]
r(10)=[-0.00 -0.00  1.00], r(11)=[-0.00  0.00  1.00], r(12)=[ 0.00 -1.00  0.00]
      [ 1.00  0.00  0.00]        [ 0.00 -1.00  0.00]        [-1.00  0.00  0.00]

      [-0.00  0.00 -1.00]        [-0.00  1.00 -0.00]        [ 1.00  0.00 -0.00]
r(13)=[-1.00 -0.00  0.00], r(14)=[-0.00 -0.00 -1.00], r(15)=[-0.00  0.00 -1.00]
      [-0.00  1.00  0.00]        [-1.00  0.00  0.00]        [-0.00  1.00  0.00]

      [ 0.00 -1.00 -0.00]        [-1.00 -0.00 -0.00]        [ 0.00 -0.00  1.00]
r(16)=[ 0.00  0.00 -1.00], r(17)=[ 0.00 -0.00 -1.00], r(18)=[ 1.00  0.00  0.00]
      [ 1.00  0.00  0.00]        [ 0.00 -1.00  0.00]        [-0.00  1.00  0.00]

      [-0.00 -0.00  1.00]        [-0.00  0.00  1.00]        [-0.00  1.00  0.00]
r(19)=[ 0.00 -1.00  0.00], r(20)=[-1.00 -0.00  0.00], r(21)=[ 1.00  0.00  0.00]
      [ 1.00  0.00  0.00]        [ 0.00 -1.00  0.00]        [-0.00  0.00 -1.00]

      [ 1.00  0.00  0.00]        [ 0.00 -1.00  0.00]        [-0.00  0.00 -1.00]
r(22)=[ 0.00 -1.00  0.00], r(23)=[-1.00 -0.00  0.00], r(24)=[ 1.00  0.00  0.00]
      [ 0.00  0.00 -1.00]        [ 0.00 -0.00 -1.00]        [ 0.00 -1.00 -0.00]

      [-1.00  0.00  0.00]        [-0.00  1.00  0.00]        [ 1.00  0.00  0.00]
r(25)=[ 0.00 -1.00  0.00], r(26)=[-1.00 -0.00  0.00], r(27)=[-0.00  1.00  0.00]
      [ 0.00  0.00 -1.00]        [ 0.00  0.00 -1.00]        [ 0.00  0.00 -1.00]

      [ 0.00 -1.00  0.00]        [-0.00  0.00 -1.00]        [ 1.00  0.00 -0.00]
r(28)=[ 1.00  0.00  0.00], r(29)=[ 0.00 -1.00  0.00], r(30)=[ 0.00 -1.00  0.00]
      [ 0.00  0.00 -1.00]        [ 1.00  0.00 -0.00]        [ 0.00  0.00  1.00]

      [ 0.00  0.00  1.00]        [-0.00  1.00 -0.00]        [ 1.00  0.00 -0.00]
r(31)=[ 0.00 -1.00  0.00], r(32)=[-0.00 -0.00 -1.00], r(33)=[-0.00  0.00 -1.00]
      [-1.00  0.00  0.00]        [ 1.00  0.00 -0.00]        [ 0.00 -1.00 -0.00]

      [ 0.00 -1.00 -0.00]        [-1.00 -0.00 -0.00]        [ 0.00  0.00  1.00]
r(34)=[ 0.00  0.00 -1.00], r(35)=[ 0.00 -0.00 -1.00], r(36)=[-0.00  1.00 -0.00]
      [-1.00 -0.00 -0.00]        [-0.00  1.00 -0.00]        [ 1.00  0.00 -0.00]

      [ 0.00 -0.00  1.00]        [ 0.00 -1.00  0.00]        [-1.00 -0.00  0.00]
r(37)=[ 1.00  0.00 -0.00], r(38)=[ 0.00  0.00  1.00], r(39)=[ 0.00 -0.00  1.00]
      [ 0.00 -1.00 -0.00]        [ 1.00  0.00 -0.00]        [ 0.00 -1.00 -0.00]

      [-0.00  1.00  0.00]        [ 1.00  0.00  0.00]        [-0.00  0.00 -1.00]
r(40)=[-0.00 -0.00  1.00], r(41)=[-0.00  0.00  1.00], r(42)=[-1.00 -0.00  0.00]
      [-1.00 -0.00 -0.00]        [-0.00  1.00 -0.00]        [ 0.00 -1.00 -0.00]

      [ 0.00  0.00 -1.00]        [ 0.00 -0.00 -1.00]        [ 0.00 -1.00 -0.00]
r(43)=[-0.00  1.00  0.00], r(44)=[ 1.00  0.00  0.00], r(45)=[-1.00 -0.00  0.00]
      [-1.00 -0.00 -0.00]        [-0.00  1.00 -0.00]        [ 0.00 -0.00  1.00]

      [-1.00 -0.00 -0.00]        [-0.00  1.00 -0.00]        [ 0.00 -0.00  1.00]
r(46)=[-0.00  1.00  0.00], r(47)=[ 1.00  0.00  0.00], r(48)=[-1.00 -0.00  0.00]
      [-0.00 -0.00  1.00]        [-0.00  0.00  1.00]        [-0.00  1.00  0.00]

--------------------------------------------------------------------------------

   ********************************************************************
   *                                                                  *
   *   LibXC is used for evaluating exchange-correlation functional   *
   *                      LibXC version:  5.0.0                       *
   *                                                                  *
   ********************************************************************

Functional name: LDA_X                                   
This functional 'Slater exchange' is an exchange functional, it belongs to the 'LDA' family and is defined in the reference(s):
[1] P. A. M. Dirac, Math. Proc. Cambridge Philos. Soc. 26, 376 (1930)
[2] F. Bloch, Z. Phys. 57, 545 (1929)

Functional name: LDA_C_VBH                               
This functional 'von Barth & Hedin' is a correlation functional, it belongs to the 'LDA' family and is defined in the reference(s):
[1] U. von Barth and L. Hedin, J. Phys. C: Solid State Phys. 5, 1629 (1972)

  =========================================
  Exchange-Correlation Functional Type: LDA
  =========================================


 Initial Fermi energy read from the potential:  0.64178142
MyPE, MyPEinEGroup, NumPEsInEGroup =     0    0    1
MyPE, MyPEinEGroup, NumPEsInEGroup =     0    0    1

================================================================================
Time:: Start-up         :     0.80600Sec
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------

                     *************************************
                     * Moment Info Output from printAtom *
                     *************************************

================================================================================
Global Index    :      1
Local Moment    :   0.00000000
Local evec_old  :   0.00000000  0.00000000  1.00000000
Local evec_new  :   0.00000000  0.00000000  1.00000000
Local evec_out  :   0.00000000  0.00000000  1.00000000
Constrain Fld   :   0.00000000  0.00000000  0.00000000
Moment    Mixing Parameter:  0.10000
Evec      Mixing Algorithm:  0.00000
================================================================================


********************************************************************************
                            SCF Iteration Number:   1
********************************************************************************

Here is the architecture/linux-intel-nogpu file.

$ pwd
/home/USERNAME/softwares/MuST-1.8.3.6-ps2018/architecture
$ cat linux-intel-nogpu 
#=====================================================================
# Acceleration = 1: enable GPU acceleration
# Acceleration = 0: otherwise
#=====================================================================
Acceleration = 0

#=====================================================================
# Library paths and elements, e.g.,
#    HDF5_PATH   = /opt/packages/HDF5/hdf5-1.10.5
#    LIBXC_PATH  = /opt/packages/LibXC/libxc-4.3.4/INTEL
#    ACCEL_PATH  = /usr/local/cuda
#    FFTW_PATH   = /usr/local/FFTW/fftw-3.3.8/INTEL
#    P3DFFT_PATH = /opt/packages/P3DFFT/p3dfft-2.7.9/INTEL
#    LUA_PATH    = /opt/packages/Lua/lua-5.3.5
#  
# If LUA_PATH, LIBXC_PATH, FFTW_PATH, and/or P3DFFT_PATH are empty, the
# corresponding packages will be installed under $(EXTERN_LIB_PATH)
#=====================================================================
HDF5_PATH   = 
ACCEL       = CUDA
ACCEL_PATH  = /usr/local/cuda
LIBXC_PATH  =
FFTW_PATH   =
P3DFFT_PATH =
LUA_PATH    =
LIBS       += -mkl=cluster -lifcore

#=====================================================================
# Compiler tools
#=====================================================================
CC          = mpiicc
CXX         = mpiicpc
F77         = mpiifort
FC          = mpiifort
MPICC       = mpiicc
ACCEL_CXX   = nvcc -arch=sm_35
ARCHV       = xiar -r

#=====================================================================
# Preprocessor/Compiler/Linker flags, e.g.,
FFLAGS = -I. -O3 -CB -CU -traceback -ftrapuv -fpe0 -ftz -fp-stack-check
# Note: "FPPFLAGS = -DMPI" enables MPI parallel processing.
#=====================================================================
FPPDEFS     = -fpp
CPPDEFS     = -cpp
FPPFLAGS    = -DMPI -DMaxOutProcs=1 -DUSE_SCALAPACK

CFLAGS      = -O3
CXXFLAGS    = -O3 -std=c++14
#FFLAGS      = -O3
OPT_OPENMP  = -qopenmp

LD_FLAGS    =
LD          = $(FC) $(LD_FLAGS)

#=====================================================================
# LIBXC_CONFIG_FLAGS, P3DFFT_CONFIG_FLAGS and FFTW_CONFIG_FLAGS are 
# ./configure flags for hdf5, libxc, p3dfft, and fftw package, respectively.
# Note: for hdf5, "--enable-parallel" might be needed in the future.
#=====================================================================
HDF5_CONFIG_FLAGS   = --enable-fortran --enable-static-exec CC=$(CC) CXX=$(CXX) FC=$(FC)
LIBXC_CONFIG_FLAGS  = CC=$(CC) CFLAGS="$(CFLAGS)" FC=$(FC) FFLAGS="$(FFLAGS)"
P3DFFT_CONFIG_FLAGS = --enable-intel FC=$(FC) CC=$(CC)
FFTW_CONFIG_FLAGS   = --enable-mpi --enable-openmp --enable-threads CC=$(CC) CFLAGS="$(CFLAGS)" MPICC=$(MPICC) F77=$(F77) FFLAGS="$(FFLAGS)"

@wangy2014
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I have not been able to reproduce your error on my local clusters, even with an old intel compiler (19.1). I suspect that the intel compiler you are using is problematic. I would recommend you try a different compiler, for example gfortran, together with openMPI built with the compiler you use. Both gcc/gfortran and openMPI are open source. You also need to have access to the BLAS, LAPACK, and ScaLAPACK libraries.

@KylinGuo
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KylinGuo commented Dec 3, 2022

problematic

Dear Wang, thanks for your suggestions. And can I expect that using this configuration will not lead to a significant performance loss?

@KylinGuo
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KylinGuo commented Dec 3, 2022

problematic

Dear Wang, thanks for your suggestions. And can I expect that using this configuration will not lead to a significant performance loss?

Dear Wang, it works now after I switch to oneapi. Thank you!

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