Welcome to the forums. Please post in English or French.

You are not logged in.

#26 2020-10-02 03:42:42

linctus
Member
Registered: 2011-11-02
Posts: 27

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

Hi there,

The error occurred during compilation and the config.log file doesn't help in this circumstance. I don't have any idea of this

build the elements catalog elem.1 using installed aster (from /tmp/install_aster.11869/aster-14.4.0/build/std/release/catalo/cata_ele.ojb)
stdout:
stderr: Segmentation fault (core dumped)

error yet but could you please attach the setup.log file? Let's see if there is any clue there.

Offline

#27 2020-10-02 08:16:56

sameer21101970
Member
Registered: 2019-09-06
Posts: 246

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

kindly refer attachment.


>>> Building the product <<<

entering directory '/tmp/install_aster.11869/aster-14.4.0'
Command line : export PATH=/tmp/tmpxvnzaauj:${PATH} ; ./waf build
compiling aster...                                                     
Command output :
compiling aster...                                                     [  OK  ]
leaving directory '/tmp/install_aster.11869/aster-14.4.0'

>>> Installation <<<

entering directory '/tmp/install_aster.11869/aster-14.4.0'
Command line : export PATH=/tmp/tmpxvnzaauj:${PATH} ; ./waf install
installing aster to /opt/aster...                                     
Command output :
installing aster to /opt/aster...                                      [FAILED]
Exit code : 1
checking environment... already set
executing: ./waf.engine install --out=build/std --jobs=4
Waf: Entering directory `/tmp/install_aster.11869/aster-14.4.0/build/std/release'


Attachments:
setup.log, Size: 1.11 MiB, Downloads: 20

Offline

#28 2020-10-03 14:26:33

sameer21101970
Member
Registered: 2019-09-06
Posts: 246

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

Dear Mr. linctus,

I look Forward to your solution to problem i am facing.

Thanks in advance

Offline

#29 2020-10-11 08:38:59

linctus
Member
Registered: 2011-11-02
Posts: 27

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

Hello there,

Sorry for not responding earlier. We just had a one-week vacation here.
From the setup log the installation of aster itself was successful but it failed to build something after that (log file line 13534~13536).
As far as I can tell it was trying to build a file named elem.1 with this command (setup.log, line 13544):

${BINDIR}/aster /opt/aster/14.4/lib/aster/Execution/E_SUPERV.py -commandes /tmp/install_aster.11869/aster-14.4.0/build/std/release/fort.1 -memjeveux 500 -tpmax 120

the fort.1 file above is just a comm file with simple contents of (guess from aster-14.4.0/catalo/wscript, line 103-106)

DEBUT(CATALOGUE=_F(FICHIER='CATAELEM', UNITE=4), 
             ERREUR=_F(ERREUR_F='ABORT'), PAR_LOT='NON')
MAJ_CATA(ELEMENT=_F())
FIN()

Indeed there is a 'elem.1' file (35 Mb or so) in the $ASTER_ROOT/14.4/lib/aster directory of my installation. And I guess you don't have it in your installation yet, right?

Unfortunately there is no other information of this 'core dump' failure in the setup log file. And I totally have no idea of such 'segment fault' and 'core dump' thing. A google search (w_w_w.geeksforgeeks.org/core-dump-segmentation-fault-c-cpp/) tells that

Core Dump/Segmentation fault is a specific kind of error caused by accessing memory that “does not belong to you.”
・When a piece of code tries to do read and write operation in a read only location in memory or freed block of memory, it is known as core dump.
・It is an error indicating memory corruption.

I am sorry that this thing is far beyond my knowledge. Just some thoughts:
(1) Is there any other log file in /tmp/install_aster.11869/aster-14.4.0 or /tmp/install_aster.11869/aster-14.4.0/build/std/release directory? Usually an aster command generates 3 or 4 log files. If there exists such log files maybe it's possible to track down what caused 'core dump' error.
(2) Your computer has 2 cores (setup.log, line 39),

Checking for number of processors (core)... 2 (will use: make -j 2)

but it tried to install aster with 4 cores (setup.log, line 936)

executing: ./waf.engine install --out=build/std --jobs=4

Could that lead to a 'core dump' problem?
(3) I remember your 'libx32' issue before and you have removed libc6-dev-x32 package. Did you also remove relative package libc6-x32? Maybe it's necessary to remove it too?

I don't have the answers, all are my guess.

Best regards,

Offline

#30 2020-10-12 09:54:33

sameer21101970
Member
Registered: 2019-09-06
Posts: 246

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

/tmp/install_aster.2296/aster-14.4.0/build/std

config.log
.lock-std_build
release folder

are generated

removed libc6-x32 completely.


Attachments:
config.log, Size: 353.06 KiB, Downloads: 15

Offline

#31 2020-10-12 10:20:04

sameer21101970
Member
Registered: 2019-09-06
Posts: 246

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

Waf: Leaving directory `/tmp/install_aster.2296/aster-14.4.0/build/std/release'
+ build the elements catalog elem.1 using installed aster (from /tmp/install_aster.2296/aster-14.4.0/build/std/release/catalo/cata_ele.ojb)


Attachments:
build_cata.py, Size: 2.27 KiB, Downloads: 11

Offline

#32 2020-10-13 03:38:06

linctus
Member
Registered: 2011-11-02
Posts: 27

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

Hi sameer,

I think the build of cata_ele.ojb was successful (you can check if the file is in /tmp/install_aster.2296/aster-14.4.0/build/std/release/catalo and its size is not zero). The problem is the next step: build elem.1 from this cata_ele.ojb by aster. Can you try to run the script below and upload the generated log file build_elem.log here? Let's hope there is some useful information in that.

#!/bin/bash
BINDIR="/opt/aster/14.4/bin"
LIBDIR="/opt/aster/14.4/lib"
PYTHONDIR="/opt/aster/14.4/lib/python3.6/site-packages"
export LD_LIBRARY_PATH="/opt/aster/public/hdf5-1.10.3/lib:/opt/aster/public/med-4.0.0/lib:/opt/aster/public/mumps-5.1.2/lib:/opt/aster/public/metis-5.1.0/lib:/opt/aster/public/tfel-3.2.1/lib:/opt/aster/public/scotch-6.0.4/lib:/opt/aster/public/hdf5-1.10.3/lib64:/opt/aster/public/med-4.0.0/lib64:/opt/aster/14.4/lib:/opt/aster/14.4/lib/aster:/home/sameer/Install_Files/aster-full-src-14.4.0:/usr:/usr/lib/gcc/x86_64-linux-gnu/7:/usr/lib/python3.6/config-3.6m-x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/opt/aster/public/tfel-3.2.1/lib:/opt/aster/public/tfel-3.2.1"
export PYTHONPATH="/opt/aster/14.4/lib/aster:/home/sameer/Install_Files/aster-full-src-14.4.0:/opt/aster/lib/python3.6/site-packages:/opt/aster/public/tfel-3.2.1/lib/python3.6/site-packages"
${BINDIR}/aster /opt/aster/14.4/lib/aster/Execution/E_SUPERV.py -commandes /tmp/install_aster.2296/aster-14.4.0/build/std/release/fort.1 -memjeveux 500 -tpmax 120 > build_elem.log 2>&1

(1) copy the code above to a text editor and save it to /tmp/install_aster.2296/aster-14.4.0 with a name, say, build_elem.sh
(2) cd /tmp/install_aster.2296/aster-14.4.0
(3) chmod +x build_elem.sh
(4) run it by ./build_elem.sh, and a file named build_elem.log should be generated
(5) upload build_elem.log here.

Best regards

Offline

#33 2020-10-13 10:58:48

sameer21101970
Member
Registered: 2019-09-06
Posts: 246

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

following error generated . build_elem.log is size 0kb.
cata_ele.ojb is 30 MB

sameer@sameer-desktop:/tmp/install_aster.4558/aster-14.4.0$ ./build_elem.sh
./build_elem.sh: line 7: 14469 Segmentation fault      (core dumped) ${BINDIR}/aster /opt/aster/14.4/lib/aster/Execution/E_SUPERV.py -commandes /tmp/install_aster.4558/aster-14.4.0/build/std/release/fort.1 -memjeveux 500 -tpmax 120

Offline

#34 2020-10-13 11:02:44

sameer21101970
Member
Registered: 2019-09-06
Posts: 246

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

+ install /opt/aster/14.4/share/aster/tests/zzzz413b.med (from astest/zzzz413b.med)
+ install /opt/aster/14.4/share/aster/tests/zzzz413c.com1 (from astest/zzzz413c.com1)
+ install /opt/aster/14.4/share/aster/tests/zzzz413c.comm (from astest/zzzz413c.comm)
+ install /opt/aster/14.4/share/aster/tests/zzzz413c.export (from astest/zzzz413c.export)
+ install /opt/aster/14.4/share/aster/tests/zzzz413c.med (from astest/zzzz413c.med)
+ install /opt/aster/14.4/share/aster/tests/zzzz414a.comm (from astest/zzzz414a.comm)
+ install /opt/aster/14.4/share/aster/tests/zzzz414a.export (from astest/zzzz414a.export)
Waf: Leaving directory `/tmp/install_aster.4558/aster-14.4.0/build/std/release'
+ build the elements catalog elem.1 using installed aster (from /tmp/install_aster.4558/aster-14.4.0/build/std/release/catalo/cata_ele.ojb)
stdout:
stderr: Segmentation fault (core dumped)

To run manually, use:
BINDIR="/opt/aster/14.4/bin"
LIBDIR="/opt/aster/14.4/lib"
PYTHONDIR="/opt/aster/14.4/lib/python3.6/site-packages"
export LD_LIBRARY_PATH="/opt/aster/public/hdf5-1.10.3/lib:/opt/aster/public/med-4.0.0/lib:/opt/aster/public/mumps-5.1.2/lib:/opt/aster/public/metis-5.1.0/lib:/opt/aster/public/tfel-3.2.1/lib:/opt/aster/public/scotch-6.0.4/lib:/opt/aster/public/hdf5-1.10.3/lib64:/opt/aster/public/med-4.0.0/lib64:/opt/aster/14.4/lib:/opt/aster/14.4/lib/aster:/home/sameer/Install_Files/aster-full-src-14.4.0:/usr:/usr/lib/gcc/x86_64-linux-gnu/7:/usr/lib/python3.6/config-3.6m-x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/opt/aster/public/tfel-3.2.1/lib:/opt/aster/public/tfel-3.2.1"
export PYTHONPATH="/opt/aster/14.4/lib/aster:/home/sameer/Install_Files/aster-full-src-14.4.0:/opt/aster/lib/python3.6/site-packages:/opt/aster/public/tfel-3.2.1/lib/python3.6/site-packages"
${BINDIR}/aster /opt/aster/14.4/lib/aster/Execution/E_SUPERV.py -commandes /tmp/install_aster.4558/aster-14.4.0/build/std/release/fort.1 -memjeveux 500 -tpmax 120
Command 'LD_LIBRARY_PATH="/opt/aster/public/hdf5-1.10.3/lib:/opt/aster/public/med-4.0.0/lib:/opt/aster/public/mumps-5.1.2/lib:/opt/aster/public/metis-5.1.0/lib:/opt/aster/public/tfel-3.2.1/lib:/opt/aster/public/scotch-6.0.4/lib:/opt/aster/public/hdf5-1.10.3/lib64:/opt/aster/public/med-4.0.0/lib64:/opt/aster/14.4/lib:/opt/aster/14.4/lib/aster:/home/sameer/Install_Files/aster-full-src-14.4.0:/usr:/usr/lib/gcc/x86_64-linux-gnu/7:/usr/lib/python3.6/config-3.6m-x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/opt/aster/public/tfel-3.2.1/lib:/opt/aster/public/tfel-3.2.1" ${BINDIR}/aster /opt/aster/14.4/lib/aster/Execution/E_SUPERV.py -commandes /tmp/install_aster.4558/aster-14.4.0/build/std/release/fort.1 -memjeveux 500 -tpmax 120' returned 139
EXIT_COMMAND_4558_00000106=1

*** Exception raised : error during installation

Offline

#35 2020-10-14 04:45:46

linctus
Member
Registered: 2011-11-02
Posts: 27

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

You have to run the script in the right /tmp/install_aster.**** directory.
If you are in /tmp/install_aster.4558 now, please modify the last line in the script install_elem.sh, change /tmp/install_aster.2296 to /tmp/install_aster.4558. If you have a new /tmp/install_aster.**** directory, please put /tmp/install_aster.**** in the script. This way, a proper (non-empty) build_elem.log file can be expected.

Offline

#36 2020-10-14 13:23:50

sameer21101970
Member
Registered: 2019-09-06
Posts: 246

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

all changes were made, before running command
following error generated . build_elem.log is size 0kb.
cata_ele.ojb is 30 MB

sameer@sameer-desktop:/tmp/install_aster.4558/aster-14.4.0$ ./build_elem.sh
./build_elem.sh: line 7: 14469 Segmentation fault      (core dumped) ${BINDIR}/aster /opt/aster/14.4/lib/aster/Execution/E_SUPERV.py -commandes /tmp/install_aster.4558/aster-14.4.0/build/std/release/fort.1 -memjeveux 500 -tpmax 120

I will retry tomorrow.

Last edited by sameer21101970 (2020-10-14 15:48:25)

Offline

#37 2020-10-15 03:23:07

linctus
Member
Registered: 2011-11-02
Posts: 27

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

sameer21101970 wrote:

all changes were made, before running command
following error generated . build_elem.log is size 0kb.

Weird. The aster binary should print some head information even when the execution fails. Why does your aster provide nothing? Anyway we need some information about what happens when the command is executed or we cannot find out the problem. Can you check this?
(1)

ls -l /opt/aster/14.4/bin/aster

iIt should be the size of 60Mb or so.
(2)

ldd /opt/aster/14.4/bin/aster

What is the output? Does it look reasonably?
(3)run a test case, say, forma02a, by as_run

/opt/aster/bin/as_run --vers=14.4 --test forma02a > test.log 2>&1

What does the test.log file looks like? Please upload test.log if it is not empty.

Offline

#38 2020-10-15 08:09:05

sameer21101970
Member
Registered: 2019-09-06
Posts: 246

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

Below is Terminal output. TEST LOG GENERATED. REFER SECOND MESSAGE.

sameer@sameer-desktop:~$ ls -l /opt/aster/14.4/bin/aster
-rwxr-xr-x 1 sameer sameer 38042784 Oct 15 13:35 /opt/aster/14.4/bin/aster
sameer@sameer-desktop:~$ ldd /opt/aster/14.4/bin/aster
    linux-vdso.so.1 (0x00007ffe21ba1000)
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f23aa514000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f23aa310000)
    libpython3.6m.so.1.0 => /usr/lib/x86_64-linux-gnu/libpython3.6m.so.1.0 (0x00007f23a9c65000)
    libgfortran.so.4 => /usr/lib/x86_64-linux-gnu/libgfortran.so.4 (0x00007f23a9886000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f23a94e8000)
    libmed.so.11 => not found
    libhdf5.so.103 => not found
    libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f23a915f000)
    libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007f23a8f30000)
    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f23a8d18000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f23a8927000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f23acc11000)
    libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1 (0x00007f23a86f5000)
    libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f23a84d8000)
    libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f23a82d5000)
    libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007f23a8095000)
sameer@sameer-desktop:~$ cd opt
bash: cd: opt: No such file or directory
sameer@sameer-desktop:~$ cd /opt/
sameer@sameer-desktop:/opt$ cd aster
sameer@sameer-desktop:/opt/aster$ cd bin
sameer@sameer-desktop:/opt/aster/bin$ ./as_run --vers=14.4 --test forma02a > test.log 2>&1
sameer@sameer-desktop:/opt/aster/bin$

Last edited by sameer21101970 (2020-10-15 09:45:29)

Offline

#39 2020-10-15 09:46:19

sameer21101970
Member
Registered: 2019-09-06
Posts: 246

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

test.log refer attachment


Attachments:
test.log, Size: 3.57 KiB, Downloads: 10

Offline

#40 2020-10-15 13:54:12

linctus
Member
Registered: 2011-11-02
Posts: 27

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

Sorry I was posting too quickly.
What we are trying to do is to trigger 'core dumped' error by as_run a test case and save information to a test.log file. We are expecting the process goes far at least to this step:

/opt/Apps/aster/14.4/bin/aster /opt/aster/14.4/lib/aster/Execution/E_SUPERV.py -commandes fort.1 ......--memjeveux=*** --tpmax=***

Unfortunately your last try ended up before this  step because '--vers=14.4' is not working.
(1) check if file 'aster' and 'profile.sh' is in '/opt/aster/etc/codeaster' directory
(2) check if file 'config.txt' and 'profile.sh' is in '/opt/aster/14.4/share/aster' directory
(3) if yes, run test again

as_run --test forma02a > test.log 2>&1

without the '--vers=14.4' argument.

By the way, from last test.log you have 2 cores and 4G memory. Memory allocation could be a cause of core dumped error. But we need to gather log information first.

Offline

#41 2020-10-16 08:41:15

sameer21101970
Member
Registered: 2019-09-06
Posts: 246

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

(1) check if file 'aster' and 'profile.sh' is in '/opt/aster/etc/codeaster' directory : YES EXIST
(2) check if file 'config.txt' and 'profile.sh' is in '/opt/aster/14.4/share/aster' directory : YES EXIST
(3) if yes, run test again
sameer@sameer-desktop:/opt/aster/bin$ as_run --test forma02a > test.log 2>&1

OUTPUT MESSAGE in test.log is as under
Command 'as_run' not found, but can be installed with:
sudo apt install code-aster-run

SO Below Command was run,
sameer@sameer-desktop:/opt/aster/bin$ ./as_run --test forma02a > test.log 2>&1

the test.log file generated from above command is attached herewith.

Thanks for your time & effort.
My Intrest is Petsc solver.


Attachments:
test.log, Size: 3.56 KiB, Downloads: 10

Offline

#42 2020-10-16 10:13:48

linctus
Member
Registered: 2011-11-02
Posts: 27

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

Oh no, aster still didn't find the version properly. Can you post the content of '/opt/aster/etc/aster' first? It's a simple text file.

Offline

#43 2020-10-16 12:59:00

sameer21101970
Member
Registered: 2019-09-06
Posts: 246

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

file at below location
/opt/aster/etc/codeaster/aster

# Code_Aster versions
# versions can be absolute paths or relative to ASTER_ROOT
# examples : NEW11, /usr/lib/codeaster/NEW11

# default version (overridden by --vers option)
default_vers : stable

# available versions
# DO NOT EDIT FOLLOWING LINE !
#?vers : VVV?

Offline

#44 2020-10-16 14:24:33

linctus
Member
Registered: 2011-11-02
Posts: 27

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

Add a line

vers : stable:/opt/aster/14.4/share/aster

at the end of '/opt/aster/etc/aster', save it, and run

as_run --test forma02a > test.log 2>&1

again.

Offline

#45 2020-10-16 15:51:22

sameer21101970
Member
Registered: 2019-09-06
Posts: 246

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

refer attachment

i always have to run
./as_run --test forma02a > test.log 2>&1 command


Attachments:
test.log, Size: 30.07 KiB, Downloads: 7

Offline

#46 2020-10-18 11:36:55

linctus
Member
Registered: 2011-11-02
Posts: 27

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

Hello sameer,

The core dumped error was reproduced by as_run test case forma02a. The error occurred as soon as the '/opt/aster/14.4/bin/aster /opt/aster/14.4/lib/aster/Execution/E_SUPERV.py -commandes fort.1 .....' command was executed, like what happened in the case of building elem.1 during your installation. Below is relative information in test.log file (line 554~578):

Code_Aster run

<INFO> Command line 1 :
<INFO> /opt/aster/14.4/bin/aster /opt/aster/14.4/lib/aster/Execution/E_SUPERV.py -commandes fort.1 --num_job=20425 --mode=interactif --rep_outils=/opt/aster/outils --rep_mat=/opt/aster/14.4/share/aster/materiau --rep_dex=/opt/aster/14.4/share/aster/datg --numthreads=1 --suivi_batch --memjeveux=95.25 --tpmax=60.0

>>> 2020/10/16-20:11:43.464  [Shell@/opt/aster/lib/python3.6/site-packages/asrun/system.py:519]
remote command ( <> sameer-desktop and sameer <> sameer) ? False

>>> 2020/10/16-20:11:43.464  [execute@/opt/aster/lib/python3.6/site-packages/asrun/execution.py:377]
cmd :
( /opt/aster/14.4/bin/aster /opt/aster/14.4/lib/aster/Execution/E_SUPERV.py -commandes fort.1 --num_job=20425 --mode=interactif --rep_outils=/opt/aster/outils --rep_mat=/opt/aster/14.4/share/aster/materiau --rep_dex=/opt/aster/14.4/share/aster/datg --numthreads=1 --suivi_batch --memjeveux=95.25 --tpmax=60.0 ; echo EXECUTION_CODE_ASTER_EXIT_20425=$? ) | tee fort.6 ; exit `grep -a EXECUTION_CODE_ASTER_EXIT_20425 fort.6 | head -1 | sed -e 's/EXECUTION_CODE_ASTER_EXIT_20425=//'`
background : False
follow_output : True
Segmentation fault (core dumped)
EXECUTION_CODE_ASTER_EXIT_20425=139

>>> 2020/10/16-20:11:50.721  [local_shell@/opt/aster/lib/python3.6/site-packages/asrun/system.py:335]
    ERROR : iret = 139
    +++ STANDARD OUTPUT:
    Segmentation fault (core dumped)
    EXECUTION_CODE_ASTER_EXIT_20425=139
   
    +++ STANDARD ERROR:
   
    +++ END

Unfortunately digging deeper by this information is beyond what I am capable of. Maybe it's time to ask some developers or someone who is familiar with such things.

If there is anything else comes to my mind, it is that '/opt/aster/14.4/bin/aster' binary in my installation (Ubuntu 18.04, Gnome) is about 60Mb, but it's only 33Mb in yours. I am not sure it's a problem or not because your output of 'ldd aster' looks like usual. But 33Mb vs 60Mb is a considerable difference right?
What happens if you run '/opt/aster/14.4/bin/aster --help'? Export environments before running it.

export LD_LIBRARY_PATH="/opt/aster/public/hdf5-1.10.3/lib:/opt/aster/public/med-4.0.0/lib:/opt/aster/public/mumps-5.1.2/lib:/opt/aster/public/metis-5.1.0/lib:/opt/aster/public/tfel-3.2.1/lib:/opt/aster/public/scotch-6.0.4/lib:/opt/aster/public/hdf5-1.10.3/lib64:/opt/aster/public/med-4.0.0/lib64:/opt/aster/14.4/lib:/opt/aster/14.4/lib/aster:/home/sameer/Install_Files/aster-full-src-14.4.0:/usr:/usr/lib/gcc/x86_64-linux-gnu/7:/usr/lib/python3.6/config-3.6m-x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/opt/aster/public/tfel-3.2.1/lib:/opt/aster/public/tfel-3.2.1"
export PYTHONPATH="/opt/aster/14.4/lib/aster:/home/sameer/Install_Files/aster-full-src-14.4.0:/opt/aster/lib/python3.6/site-packages:/opt/aster/public/tfel-3.2.1/lib/python3.6/site-packages"

Good luck!

Offline

#47 2020-10-19 07:37:03

sameer21101970
Member
Registered: 2019-09-06
Posts: 246

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

sameer@sameer-desktop:/opt/aster/14.4/bin$ cd aster
bash: cd: aster: Not a directory
sameer@sameer-desktop:/opt/aster/14.4/bin$

cd aster not accepting....
this aster file size is 33.8 MB

screen shot attached.

I have download Code-Aster 14.4 from codeaster website or is there some other location of download for parallel version.

Last edited by sameer21101970 (2020-10-19 09:09:33)


Attachments:
Screenshot from 2020-10-19 12-06-23.png, Size: 8.52 KiB, Downloads: 5

Offline

#48 2020-10-19 12:35:23

linctus
Member
Registered: 2011-11-02
Posts: 27

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

'/opt/aster/14.4/bin/aster' is a file not a directory so 'cd aster' doesn't make sense. Please try this:

export LD_LIBRARY_PATH="/opt/aster/public/hdf5-1.10.3/lib:/opt/aster/public/med-4.0.0/lib:/opt/aster/public/mumps-5.1.2/lib:/opt/aster/public/metis-5.1.0/lib:/opt/aster/public/tfel-3.2.1/lib:/opt/aster/public/scotch-6.0.4/lib:/opt/aster/public/hdf5-1.10.3/lib64:/opt/aster/public/med-4.0.0/lib64:/opt/aster/14.4/lib:/opt/aster/14.4/lib/aster:/home/sameer/Install_Files/aster-full-src-14.4.0:/usr:/usr/lib/gcc/x86_64-linux-gnu/7:/usr/lib/python3.6/config-3.6m-x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/opt/aster/public/tfel-3.2.1/lib:/opt/aster/public/tfel-3.2.1"
export PYTHONPATH="/opt/aster/14.4/lib/aster:/home/sameer/Install_Files/aster-full-src-14.4.0:/opt/aster/lib/python3.6/site-packages:/opt/aster/public/tfel-3.2.1/lib/python3.6/site-packages"
/opt/aster/14.4/bin/aster --help

to see if core dumped error happens whenever '/opt/aster/bin/aster' is invoked.

Offline

#49 2020-10-19 12:55:13

sameer21101970
Member
Registered: 2019-09-06
Posts: 246

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

please refer below

sameer@sameer-desktop:~$ export LD_LIBRARY_PATH="/opt/aster/public/hdf5-1.10.3/lib:/opt/aster/public/med-4.0.0/lib:/opt/aster/public/mumps-5.1.2/lib:/opt/aster/public/metis-5.1.0/lib:/opt/aster/public/tfel-3.2.1/lib:/opt/aster/public/scotch-6.0.4/lib:/opt/aster/public/hdf5-1.10.3/lib64:/opt/aster/public/med-4.0.0/lib64:/opt/aster/14.4/lib:/opt/aster/14.4/lib/aster:/home/sameer/Install_Files/aster-full-src-14.4.0:/usr:/usr/lib/gcc/x86_64-linux-gnu/7:/usr/lib/python3.6/config-3.6m-x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/opt/aster/public/tfel-3.2.1/lib:/opt/aster/public/tfel-3.2.1"
sameer@sameer-desktop:~$ export PYTHONPATH="/opt/aster/14.4/lib/aster:/home/sameer/Install_Files/aster-full-src-14.4.0:/opt/aster/lib/python3.6/site-packages:/opt/aster/public/tfel-3.2.1/lib/python3.6/site-packages"
sameer@sameer-desktop:~$ /opt/aster/14.4/bin/aster --help
usage: /opt/aster/14.4/bin/aster [option] ... [-c cmd | -m mod | file | -] [arg] ...
Options and arguments (and corresponding environment variables):
-b     : issue warnings about str(bytes_instance), str(bytearray_instance)
         and comparing bytes/bytearray with str. (-bb: issue errors)
-B     : don't write .pyc files on import; also PYTHONDONTWRITEBYTECODE=x
-c cmd : program passed in as string (terminates option list)
-d     : debug output from parser; also PYTHONDEBUG=x
-E     : ignore PYTHON* environment variables (such as PYTHONPATH)
-h     : print this help message and exit (also --help)
-i     : inspect interactively after running script; forces a prompt even
         if stdin does not appear to be a terminal; also PYTHONINSPECT=x
-I     : isolate Python from the user's environment (implies -E and -s)
-m mod : run library module as a script (terminates option list)
-O     : remove assert and __debug__-dependent statements; add .opt-1 before
         .pyc extension; also PYTHONOPTIMIZE=x
-OO    : do -O changes and also discard docstrings; add .opt-2 before
         .pyc extension
-q     : don't print version and copyright messages on interactive startup
-s     : don't add user site directory to sys.path; also PYTHONNOUSERSITE
-S     : don't imply 'import site' on initialization
-u     : force the binary I/O layers of stdout and stderr to be unbuffered;
         stdin is always buffered; text I/O layer will be line-buffered;
         also PYTHONUNBUFFERED=x
-v     : verbose (trace import statements); also PYTHONVERBOSE=x
         can be supplied multiple times to increase verbosity
-V     : print the Python version number and exit (also --version)
         when given twice, print more information about the build
-W arg : warning control; arg is action:message:category:module:lineno
         also PYTHONWARNINGS=arg
-x     : skip first line of source, allowing use of non-Unix forms of #!cmd
-X opt : set implementation-specific option
file   : program read from script file
-      : program read from stdin (default; interactive mode if a tty)
arg ...: arguments passed to program in sys.argv[1:]

Other environment variables:
PYTHONSTARTUP: file executed on interactive startup (no default)
PYTHONPATH   : ':'-separated list of directories prefixed to the
               default module search path.  The result is sys.path.
PYTHONHOME   : alternate <prefix> directory (or <prefix>:<exec_prefix>).
               The default module search path uses <prefix>/lib/pythonX.X.
PYTHONCASEOK : ignore case in 'import' statements (Windows).
PYTHONIOENCODING: Encoding[:errors] used for stdin/stdout/stderr.
PYTHONFAULTHANDLER: dump the Python traceback on fatal errors.
PYTHONHASHSEED: if this variable is set to 'random', a random value is used
   to seed the hashes of str, bytes and datetime objects.  It can also be
   set to an integer in the range [0,4294967295] to get hash values with a
   predictable seed.
PYTHONMALLOC: set the Python memory allocators and/or install debug hooks
   on Python memory allocators. Use PYTHONMALLOC=debug to install debug
   hooks.
sameer@sameer-desktop:~$

ALSO DONE ,

sameer@sameer-desktop:~$ cd /opt/aster/14.4/bin/aster --help
bash: cd: too many arguments
sameer@sameer-desktop:~$ cd /opt/aster/14.4/bin
sameer@sameer-desktop:/opt/aster/14.4/bin$ aster --help

Command 'aster' not found, did you mean:

  command 'paster' from deb python-pastescript

Try: sudo apt install <deb name>

sameer@sameer-desktop:/opt/aster/14.4/bin$

Last edited by sameer21101970 (2020-10-19 13:24:48)

Offline

#50 2020-10-20 13:12:02

linctus
Member
Registered: 2011-11-02
Posts: 27

Re: code_aster 14.4 parallel version with PETSc - Mumps error & further he

Thanks for trying.
So the aster binary doesn't crash whenever it is invoked, at least in 'aster --help' case. But it does crash when trying to do some 'real job', at least in case of running a relative 'light' case, forma02a, and a relative 'heavy' case, building elem.1.
In both cases the similarity is that core dumped error occurs when command '/opt/aster/14.4/bin/aster /opt/aster/14.4/lib/aster/Execution/E_SUPERV.py -commandes fort.1 .....' is executed. Besides that I don't have other idea at this moment.

Offline