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#1 2018-01-04 04:17:22

JakeZwart
Member
Registered: 2012-05-25
Posts: 51

[SOLVED] Error with AsterStudy when Executing Video Tutorial

I have installed Salome-Meca LGPL 2017.0.2 on a Ubuntu 14.04 machine with the requirements listed on the installation web page and installing the libopenblas-dev package.  I have tried to follow all the commands from the video tutorial shown in the section "Learn how to use AsterStudy with video tutorials!".

When I execute the RunCase the message file shows that the first line reading the mesh executes correctly.
The problem occurs after the execution of the second line, indicating a problem with that line.  The message is:

Message file wrote:

   model = AFFE_MODELE(MAILLAGE=mesh,
                      AFFE=_F(PHENOMENE='THERMIQUE',
                              TOUT='OUI',
                              MODELISATION=('3D', ),),
                      INFO=1,
                      VERI_JACOBIEN='OUI',
                      DISTRIBUTION=_F(PARTITIONNEUR='METIS',
                                      METHODE='SOUS_DOMAINE',),
                      )


Sur les 2336 mailles du maillage mesh, on a demandé l'affectation de 2336, on a pu en affecter 2060
EXECUTION_CODE_ASTER_EXIT_3746=127

<I>_EXIT_CODE = 127

The comm file is

 rho_cp = 3710000

mesh = LIRE_MAILLAGE(UNITE=20)

model = AFFE_MODELE(
    AFFE=_F(MODELISATION=('3D', ), PHENOMENE='THERMIQUE', TOUT='OUI'),
    MAILLAGE=mesh
)

mater = DEFI_MATERIAU(THER=_F(LAMBDA=54.6, RHO_CP=rho_cp))

fieldmat = AFFE_MATERIAU(AFFE=_F(MATER=(mater, ), TOUT='OUI'), MAILLAGE=mesh)

temp_f = DEFI_FONCTION(NOM_PARA='INST', VALE=(0.0, 20.0, 10.0, 70.0))

listr = DEFI_LIST_REEL(DEBUT=0.0, INTERVALLE=_F(JUSQU_A=10.0, NOMBRE=2))

load0 = AFFE_CHAR_THER_F(
    MODELE=model, TEMP_IMPO=_F(GROUP_MA=('INNER_SKIN', ), TEMP=temp_f)
)

resther = THER_LINEAIRE(
    CHAM_MATER=fieldmat,
    ETAT_INIT=_F(VALE=20.0),
    EXCIT=_F(CHARGE=load0),
    INCREMENT=_F(LIST_INST=listr),
    MODELE=model
)

IMPR_RESU(RESU=_F(RESULTAT=resther), UNITE=80)

Thanks in advance for your help.

Last edited by JakeZwart (2018-04-12 14:13:00)

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#2 2018-01-04 09:32:50

Thomas DE SOZA
Guru
From: EDF
Registered: 2007-11-23
Posts: 2,991

Re: [SOLVED] Error with AsterStudy when Executing Video Tutorial

Hello,

Thank you for this feedback. In order to help up diagnose the problem, could you please try provide the files located in the "*_Files" folder generated alongside the HDF study file?

It may be the same error as the one reported here: https://code-aster.org/forum2/viewtopic … 626#p55626
You could try to install the "LAPACK" package and see if it solves the error.

TdS

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#3 2018-01-04 13:55:58

JakeZwart
Member
Registered: 2012-05-25
Posts: 51

Re: [SOLVED] Error with AsterStudy when Executing Video Tutorial

Thanks Thomas,

I tried installing the liblapack3 package but found it was already installed.

I have zipped and attached the requested files.


Attachments:
Pipe_Files.zip, Size: 20.38 KiB, Downloads: 25

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#4 2018-01-05 15:52:56

JakeZwart
Member
Registered: 2012-05-25
Posts: 51

Re: [SOLVED] Error with AsterStudy when Executing Video Tutorial

I have changed the  LIRE_MALLAGE command to give more information.

  mesh = LIRE_MAILLAGE(UNITE=20,
                       FORMAT='MED',
                       INFO_MED=1,
                       INFO=1,
                       VERI_MAIL=_F(APLAT=1.E-3,
                                    VERIF='OUI',),
                       )

From this I found that the elements that are read are:

NOMBRE DE NOEUDS                        1518

NOMBRE DE MAILLES                       2336
                              SEG2                  276
                              QUAD4                1160
                              HEXA8                 900

NOMBRE DE GROUPES DE MAILLES               4
                              INNER_SKIN                         450
                              TOP                                 20
                              BASE                                20
                              SYMMETRY                           180

And the next command I use (expanded with the defaults added) is

  model = AFFE_MODELE(MAILLAGE=mesh,
                      AFFE=_F(PHENOMENE='THERMIQUE',
                              TOUT='OUI',
                              MODELISATION=('3D', ),),
                      INFO=1,
                      VERI_JACOBIEN='OUI',
                      PARTITION=_F(PARALLELISME='GROUP_ELEM',),
                      )

The error I get from this command is

Sur les 2336 mailles du maillage mesh, on a demandé l'affectation de 2336, on a pu en affecter 2060
EXECUTION_CODE_ASTER_EXIT_13982=127

<I>_EXIT_CODE = 127

The difference between 2336 and 2060 is 236, the number of SEG2 elements.  So now I am trying to figure out why I have these elements.  I am assuming the error means that either these elements are not 3D (which I suspect) or that they are not thermal elements.

Since I was trying to follow the tutorial, I am curious as to why I would have this problem.  I will keep you posted on what I find.

Last edited by JakeZwart (2018-01-05 15:56:04)

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#5 2018-01-05 23:06:41

mecour
Member
Registered: 2011-04-04
Posts: 23

Re: [SOLVED] Error with AsterStudy when Executing Video Tutorial

Hello,

This is looks like some error in AsterStudy. If I use your comm file and model from tutorial in stand alone code-aster 13.4 without aster study, the computation run without error.
In another thread is the similar problem and the same solution.
https://code-aster.org/forum2/viewtopic.php?id=23047

mecour

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#6 2018-01-06 17:35:19

Thomas DE SOZA
Guru
From: EDF
Registered: 2007-11-23
Posts: 2,991

Re: [SOLVED] Error with AsterStudy when Executing Video Tutorial

Hello,

JakeZwart wrote:

I tried installing the liblapack3 package but found it was already installed.

I have zipped and attached the requested files.

mecour wrote:

This is looks like some error in AsterStudy. If I use your comm file and model from tutorial in stand alone code-aster 13.4 without aster study, the computation run without error.

Thanks for this feedback. This is then the same problem as this post and my diagnostic was wrong.

Note that this has nothing to do with AsterStudy but is rather related to the code_aster executable embedded in Salome-Meca 2017.0.2.

Could you please provide us with the outputs of the following commands ?

To look for the shared libraries used by the code_aster executable on your machine:

$ ldd /home/jake/salome_meca/V2017.0.2/tools/Code_aster_stable-v134_smeca/bin/aster

To look for the OpenBLAS library:

$ ls -l /usr/lib/libopenblas.so.0

To look for the missing symbol causing the error in the OpenBLAS Library:

 
$ nm -D /usr/lib/libopenblas.so.0 | grep -i dgesv

Best regards,
TdS

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#7 2018-01-06 18:58:18

JakeZwart
Member
Registered: 2012-05-25
Posts: 51

Re: [SOLVED] Error with AsterStudy when Executing Video Tutorial

Thanks for the reply.  I was going to try and run it using stand alone code aster but am not there yet.  In response to your query:

jake@jake-Latitude-D830:~$ ldd /home/jake/salome_meca/V2017.0.2/tools/Code_aster_stable-v134_smeca/bin/aster
    linux-vdso.so.1 =>  (0x00007ffe0cbb3000)
    libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00007fe011707000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fe011401000)
    libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007fe0111c2000)
    libhdf5.so.9.0.0 => not found
    libTFELMaterial.so => not found
    libTFELMath.so => not found
    libTFELSystem.so => not found
    libTFELUtilities.so => not found
    libTFELException.so => not found
    libAsterInterface.so => not found
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fe010fa4000)
    libopenblas.so.0 => /usr/lib/libopenblas.so.0 (0x00007fe00f79b000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fe00f597000)
    libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007fe00f394000)
    libpython2.7.so.1.0 => /usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0 (0x00007fe00ee30000)
    libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fe00eb1d000)
    libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007fe00e8ee000)
    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fe00e6d7000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fe00e30e000)
    /lib64/ld-linux-x86-64.so.2 (0x00007fe011a2e000)
    libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fe00e0f5000)

and for openblas:

jake@jake-Latitude-D830:~$ ls -l /usr/lib/libopenblas.so.0
-rw-r--r-- 1 root root 23058832 Apr  4  2014 /usr/lib/libopenblas.so.0

And the command to look for the missing symbol comes up blank:

jake@jake-Latitude-D830:~$ nm -D /usr/lib/libopenblas.so.0 | grep -i dgesv
jake@jake-Latitude-D830:~$
jake@jake-Latitude-D830:~$

Is it worth trying to set up Ubuntu 16 and trying that?

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#8 2018-01-07 16:32:13

Thomas DE SOZA
Guru
From: EDF
Registered: 2007-11-23
Posts: 2,991

Re: [SOLVED] Error with AsterStudy when Executing Video Tutorial

JakeZwart wrote:

And the command to look for the missing symbol comes up blank:

jake@jake-Latitude-D830:~$ nm -D /usr/lib/libopenblas.so.0 | grep -i dgesv
jake@jake-Latitude-D830:~$
jake@jake-Latitude-D830:~$

Interesting, this confirms that the OpenBLAS library installed on your Ubuntu 14.04 is missing the symbols from the LAPACK library.

JakeZwart wrote:

Is it worth trying to set up Ubuntu 16 and trying that?

I have to admit, this is likely a possible fix to the problem although quite impacting.
A less invasive way would be to do a manual installation of the latest OpenBLAS (see for instance https://github.com/xianyi/OpenBLAS/wiki/Faq#debianlts).

[EDIT]: the following post confirmed that the upgrade of OpenBLAS fixes the problem on Ubuntu 14.04
https://code-aster.org/forum2/viewtopic … 691#p55691

TdS

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#9 2018-01-09 03:36:17

JakeZwart
Member
Registered: 2012-05-25
Posts: 51

Re: [SOLVED] Error with AsterStudy when Executing Video Tutorial

I have been working on this with no success to date.

I have installed the openblas_xianyi library successfully.  Now I get

jake@jake-Latitude-D830:~$ nm -D /usr/lib/openblas_xianyi/lib/libopenblas.so.0 | grep -i dgesv
000000000009bf50 T dgesv_
0000000000538290 T dgesvd_
0000000000542510 T dgesvdx_
000000000062e500 T dgesvj_
0000000000544b80 T dgesvx_
0000000000adf670 T LAPACKE_dgesv
0000000000adfa10 T LAPACKE_dgesvd
0000000000adfc30 T LAPACKE_dgesvd_work
0000000000ae0300 T LAPACKE_dgesvdx
0000000000ae0620 T LAPACKE_dgesvdx_work
0000000000ae0ef0 T LAPACKE_dgesvj
0000000000ae1130 T LAPACKE_dgesvj_work
0000000000adf740 T LAPACKE_dgesv_work
0000000000ae1610 T LAPACKE_dgesvx
0000000000ae1980 T LAPACKE_dgesvx_work
jake@jake-Latitude-D830:~$

Like lzhang I put the command "export LD_LIBRARY_PATH=/usr/lib/openblas_xianyi/lib" as the last line of my ~/.bashrc file.

Unlike lzhang, there is no difference in the execution of the program.  I tried execution from within Salome-meca and using standalone code-aster.  The message files are not consistent between them.

I have attached the salome-meca files and the Code Aster files in the zip file.

I have not figured out as yet how to use the Salome-Meca shell and as_run from the command line as lzhang does.


Attachments:
Pipe1_Files.zip, Size: 55.41 KiB, Downloads: 23

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#10 2018-01-09 11:25:37

lzhang
Member
Registered: 2017-11-07
Posts: 10

Re: [SOLVED] Error with AsterStudy when Executing Video Tutorial

Hello,

You can run your simulation via the terminal by typing
/home/jake/salome_meca/appli_V2017.0.2/salome shell 'as_run solid.export',

I suppose /home/jake/salome_meca is your salome_meca2017 installation directory.

Before doing that, you can use
ldd /home/jake/salome_meca/V2017.0.2/tools/Code_aster_stable-v134_smeca/bin/aster
to make sure that the openblas library used by aster is openblas_xianyi, the one you have installed manually.

Regards,
Lei

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#11 2018-01-10 17:50:02

JakeZwart
Member
Registered: 2012-05-25
Posts: 51

Re: [SOLVED] Error with AsterStudy when Executing Video Tutorial

Thanks to all that have helped so far.

lzhang writes

Before doing that, you can use
ldd /home/jake/salome_meca/V2017.0.2/tools/Code_aster_stable-v134_smeca/bin/aster
to make sure that the openblas library used by aster is openblas_xianyi, the one you have installed manually.

The output from this command shows that the correct library is used.

jake@jake-Latitude-D830:~/salomeWork/AsterStudyPipeTutorial$ ldd /home/jake/salome_meca/V2017.0.2/tools/Code_aster_stable-v134_smeca/bin/aster
    linux-vdso.so.1 =>  (0x00007ffe843eb000)
    libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00007f19e241b000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f19e2115000)
    libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007f19e1ed6000)
    libhdf5.so.9.0.0 => not found
    libTFELMaterial.so => not found
    libTFELMath.so => not found
    libTFELSystem.so => not found
    libTFELUtilities.so => not found
    libTFELException.so => not found
    libAsterInterface.so => not found
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f19e1cb8000)
    libopenblas.so.0 => /usr/lib/openblas_xianyi/lib/libopenblas.so.0 (0x00007f19e0d96000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f19e0b92000)
    libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f19e098f000)
    libpython2.7.so.1.0 => /usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0 (0x00007f19e042b000)
    libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f19e0118000)
    libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007f19dfee9000)
    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f19dfcd2000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f19df909000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f19e2742000)
    libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f19df6f0000)
jake@jake-Latitude-D830:~/salomeWork/AsterStudyPipeTutorial$

The program is still not executing.  Any ideas?
Are the missing shared objects (.so) serious?  Or is that normal?

Last edited by JakeZwart (2018-01-10 17:55:54)

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#12 2018-01-12 19:23:16

JakeZwart
Member
Registered: 2012-05-25
Posts: 51

Re: [SOLVED] Error with AsterStudy when Executing Video Tutorial

I tried tried the tutorial at the feaforall.com website to ensure that there was not a problem with my mesh model.  It gives the same error as the previous model, confirming that there is a problem with the installation.

I checked to ensure that the files required are present in the openblas directory and they are shown below.  To me it seems like all the shared objects have execute status, so I cannot see what is wrong.  Is there another suggestion of something I should try?

jake@jake-Latitude-D830:/usr/lib/openblas_xianyi/lib$ ll
total 40972
drwxr-xr-x 4 root root     4096 Jan  8 12:19 ./
drwxr-xr-x 5 root root     4096 Jan  8 12:19 ../
drwxr-xr-x 3 root root     4096 Jan  8 12:19 cmake/
lrwxrwxrwx 1 root root       29 Jan  8 12:19 libopenblas.a -> libopenblas_penrynp-r0.2.20.a
-rw-r--r-- 1 root root 28025974 Jan  8 12:07 libopenblas_penrynp-r0.2.20.a
-rwxr-xr-x 1 root root 13907213 Jan  8 12:07 libopenblas_penrynp-r0.2.20.so*
lrwxrwxrwx 1 root root       30 Jan  8 12:19 libopenblas.so -> libopenblas_penrynp-r0.2.20.so*
lrwxrwxrwx 1 root root       30 Jan  8 12:19 libopenblas.so.0 -> libopenblas_penrynp-r0.2.20.so*
drwxr-xr-x 2 root root     4096 Jan  8 12:19 pkgconfig/
jake@jake-Latitude-D830:/usr/lib/openblas_xianyi/lib$
jake@jake-Latitude-D830:/usr/lib/openblas_xianyi/lib$
jake@jake-Latitude-D830:/usr/lib/openblas_xianyi/lib$ echo "$LD_LIBRARY_PATH"
/usr/lib/openblas_xianyi/lib
jake@jake-Latitude-D830:/usr/lib/openblas_xianyi/lib$

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#13 2018-01-15 15:47:39

Thomas DE SOZA
Guru
From: EDF
Registered: 2007-11-23
Posts: 2,991

Re: [SOLVED] Error with AsterStudy when Executing Video Tutorial

JakeZwart wrote:

Is there another suggestion of something I should try?

Try editing the following file in the installation of Salome-Meca :

../V2017.0.2/tools/Code_aster_stable-v134_smeca/share/aster/profile.sh

Then add the path to the manually installed library at the beginning as follows :

# created by waf using data/wscript



LD_LIBRARY_PATH=/usr/lib/openblas_xianyi/lib:$ASTER_VERSION_DIR/lib:\

This should hopefully force the code_aster executable to use the OpenBLAS from your installation.

TdS

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#14 2018-01-15 18:29:06

JakeZwart
Member
Registered: 2012-05-25
Posts: 51

Re: [SOLVED] Error with AsterStudy when Executing Video Tutorial

Thanks Thomas,

It now works!

I tried both the Pipe Thermal tutorial I found on your website and the Plate tutorial from the feaforall website.  Both ran successfully and the results looked correct.

However, the message that AsterStudy brings up includes a warning

AsterStudy wrote:

Run case "RunCase_1" calculations process started
Starting "RunCase_1:Stage_1"...
Stage "RunCase_1:Stage_1" start calculation (jobid=14)
Copying result u'/home/jake/salomeWork/AsterStudyPipeTutorial/pipe1.resu.med'
Stage "RunCase_1:Stage_1" calculation succeeded with state Success+Warn (272)
Run case "RunCase_1" calculations process finished

I am not sure what the significance of the warning is?

Should I mark this as solved or is this still an issue?

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#15 2018-01-16 07:26:42

jeanpierreaubry
Guru
From: nantes (france)
Registered: 2009-03-12
Posts: 3,120
Website

Re: [SOLVED] Error with AsterStudy when Executing Video Tutorial

hello

no warning
just all is sucessfull

jean pierre aubry

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