[Solved] Compile 11.0.10-2 w/ MPI, mumps & scotch (Ubuntu 11.04 64bit)

JMB365 · 2011-10-12 14:02:26

Hello all,

I am trying to compile aster-full-src-11.0.10-2.noarch.tar.gz using the broad guidelines posted at http://www.code-aster.org/forum2/viewtopic.php?id=14892 by ppeetteerr et. al. and I am stuck at the final stage of compiling CA with the error messages:

from the file /opt/aster/NEW11.0_mpi/obj/asterd/hdf.msg I have:

Messages de compilation
=======================
/opt/aster/NEW11.0_mpi/bibc/hdf/hdfopg.c: In function hdfopg_:
/opt/aster/NEW11.0_mpi/bibc/hdf/hdfopg.c:58:3: error: too few arguments to function H5Gopen2
/opt/aster/public/hdf5-1.8.4/include/H5Gpublic.h:78:14: note: declared here

/opt/aster/NEW11.0_mpi/bibc/hdf/hdfwsv.c: In function hdfwsv_:
/opt/aster/NEW11.0_mpi/bibc/hdf/hdfwsv.c:117:3: error: too few arguments to function H5Dcreate2
/opt/aster/public/hdf5-1.8.4/include/H5Dpublic.h:104:14: note: declared here

/opt/aster/NEW11.0_mpi/bibc/hdf/hdfwat.c: In function hdfwat_:
/opt/aster/NEW11.0_mpi/bibc/hdf/hdfwat.c:62:7: error: too few arguments to function H5Acreate2
/opt/aster/public/hdf5-1.8.4/include/H5Apublic.h:44:16: note: declared here

I was able to successfully compile and install the following:
mpich2-1.3.2.tar.gz
scalapack_installer_0.96.tgz
ParMetis-3.1.1.tar.gz
scotch-5.1.11_esmumps-1.tar.gz
mumps-4.9.2-2.tar.gz

The failure occurs at:
sudo ../bin/as_run --vers=NEW11.0_mpi --make

I have attached the config.txt file. If there is (are) any other file(s) I need to post please let me know. By the way a standard sequential install of CA_11.0.10-2 completed successfully on this freshly installed Ubuntu_11.04-64bit OS. Can somebody help please? Thanks!

Regards, JMB

Last edited by JMB365 (2011-10-13 02:46:01)

Attachments:
config.txt, Size: 6.7 KiB, Downloads: 646

Thomas DE SOZA · 2011-10-12 14:10:56

Hi,

2 possibilities :

- either update your NEW11 to latest. This bug was fixed in 11.0.13

- or recompile HDF5-1.8.4 using this option in configure step "--with-default-api-version=v16"

TdS

JMB365 · 2011-10-12 14:40:59

Thomas DE SOZA wrote:

Hi,
- either update your NEW11 to latest. This bug was fixed in 11.0.13
- or recompile HDF5-1.8.4 using this option in configure step "--with-default-api-version=v16"
TdS

Hello TdS,

Thank you for the extremely QUICK reply and advice !!! I really appreciate that very much! Let me try to understand the 2 choices:
1. Would mean I update NEW11 to the latest in the sequential version using standard procedure (which I do not readily remember), followed by copying it such as "sudo cp -ax NEW11.0 NEW11.0_mpi"? I presume I do not have to recompile
mpich2-1.3.2.tar.gz
scalapack_installer_0.96.tgz
ParMetis-3.1.1.tar.gz
scotch-5.1.11_esmumps-1.tar.gz
mumps-4.9.2-2.tar.gz
etc.
Am I correct?

2. About this one I am a bit lost, would you kindly elaborate how to do this? Where do I tell it use "--with-default-api-version=v16" ?

Thank you very much again for your patience and timely advice...

Best regards, JMB

Thomas DE SOZA · 2011-10-12 14:48:20

JMB365 wrote:

1. Would mean I update NEW11 to the latest in the sequential version using standard procedure (which I do not readily remember), followed by copying it such as "sudo cp -ax NEW11.0 NEW11.0_mpi"?

If you want you may directly update the NEW11.0_mpi version by doing something like "as_run --auto_update --nolocal --vers=NEW11.0_mpi"

JMB365 wrote:

2. About this one I am a bit lost, would you kindly elaborate how to do this? Where do I tell it use "--with-default-api-version=v16" ?

This is when building HDF5-1.8.4. I assumed you had built it and therefore needed to rebuild it and adding this option to the configure step.
If it is not the case then forget about this. The solution would involve modifying the aster sources which is almost identical to 1.

TdS

JMB365 · 2011-10-12 15:14:30

Thomas DE SOZA wrote:

... you may directly update the NEW11.0_mpi version by doing something like "as_run --auto_update --nolocal --vers=NEW11.0_mpi"
TdS

Hello TdS,
I tried the above. It automatically downloaded all the updates, went through the compilation process and still reports the same errors, which I had posted in my first posting. What do I do now?
Regards, JMB

Update: The same "as_run --auto_update --nolocal --vers=NEW11.0" works fine on the non-MPI version I had compiled earlier. Hope this gives you additional clues. I can post all the detailed steps if that will help diagnose it further.

Last edited by JMB365 (2011-10-12 15:33:00)

JMB365 · 2011-10-12 19:47:52

Hello,

I managed to get further in the compilation process but am stumped by the following:

testing executable /opt/aster/NEW11.0_mpi/asterd...                     [FAILED]
Exit code : 65280
invalid "local" arg: --hostfile

There is indirect reference to it here: http://www.code-aster.org/forum2/viewtopic.php?id=14892 but I do not know how I can use that info to fix a compilation problem. Any ideas?! Thanks...

Regards, JMB

Thomas DE SOZA · 2011-10-12 20:34:09

The link you posted gives the solution : you have to edit the $ASTER_ROOT/etc/codeaster/asrun config file, find the mpirun_cmd statement and make the necessary adjustments.
These adjustments depend on the MPI implementation you're using. Look in the manual of the mpirun command of your implementation and see how nodes are specified. For a first test you may omit the list of host files and run on the master node.

Note : the compilation has ended, it is only a test step, so everything else should be OK

TdS

JMB365 · 2011-10-13 00:05:02

Thomas DE SOZA wrote:

The link you posted gives the solution : you have to edit the $ASTER_ROOT/etc/codeaster/asrun config file, find the mpirun_cmd statement and make the necessary adjustments. These adjustments depend on the MPI implementation you're using. Look in the manual of the mpirun command of your implementation and see how nodes are specified. For a first test you may omit the list of host files and run on the master node. Note : the compilation has ended, it is only a test step, so everything else should be OK TdS

Hello TdS,

Actually the compilation is not okay, since there is no asteru compiled, only the asterd is present. But I appreciate the advice you have given about modifying the $ASTER_ROOT/etc/codeaster/asrun config. And it worked! I have an asterd_mpi - Hurrah! Thanks!

Regards, JMB

Last edited by JMB365 (2011-10-13 01:13:37)

JMB365 · 2011-10-13 02:24:38

Now that I have successfully compiled the mpi versions of CodeAster. Now I have some simple questions:

In another post I found in the config.txt file for the mpi compilation containing:

BINCMDE        | bin     | 11-04 | mpi/commande
BINELE         | bin     | 11-04 | mpi/elements
BINPICKLED     | bin     | 11-04 | mpi/cata_ele.pickled
BINLIB_NODBG   | bin     | 11-04 | mpi/lib/libaster.a
BINLIB_DBG     | bin     | 11-04 | mpi/lib/libasterd.a
BINLIBF_NODBG  | bin     | 02-05 | mpi/lib/libferm.a
BINLIBF_DBG    | bin     | 02-05 | mpi/lib/libfermd.a
BINOBJ_NODBG   | bin     | 11-04 | mpi/obj/aster
BINOBJF_NODBG  | bin     | 11-04 | mpi/obj/ferm
BINOBJ_DBG     | bin     | 11-04 | mpi/obj/asterd
BINOBJF_DBG    | bin     | 11-04 | mpi/obj/fermd

(Note the mpi/ in front of all the paths.)
Would this be appropriate when the sequential aster executables and the mpi ones happen to be in a SINGLE subdirectory /opt/aster/NEW11.0 subdirectory, such as:
asteru
asterd
asteru_mpi
asterd_mpi
(with all their respective support stuff being in the same /opt/aster/NEW11.0 but in separate subdirectories within such as lib, obj and mpi/lib, mpi/obj respectively)?

Whereas I have used:

BINCMDE        | bin     | 11-04 | commande
BINELE         | bin     | 11-04 | elements
BINPICKLED     | bin     | 11-04 | cata_ele.pickled
BINLIB_NODBG   | bin     | 11-04 | lib/libaster.a
BINLIB_DBG     | bin     | 11-04 | lib/libasterd.a
BINLIBF_NODBG  | bin     | 02-05 | lib/libferm.a
BINLIBF_DBG    | bin     | 02-05 | lib/libfermd.a
BINOBJ_NODBG   | bin     | 11-04 | obj/aster
BINOBJF_NODBG  | bin     | 11-04 | obj/ferm
BINOBJ_DBG     | bin     | 11-04 | obj/asterd
BINOBJF_DBG    | bin     | 11-04 | obj/fermd

But I have chosen to create two COMPLETELY separate sub-directories /opt/aster/NEW11.0 and opt/aster/NEW11.0_mpi...

I am trying to understand the difference between the two methodologies. Is one way better than the other? I am doing this (MPI compilation) for the first time so, please be patient with me. Thanks!

Regards, JMB

Last edited by JMB365 (2011-10-13 02:29:39)

Thomas DE SOZA · 2011-10-13 08:54:18

What you have done is OK. It is always better to handle 2 differents directories. The only thing better you can do is : instead of duplicating NEW11 to NEW11_mpi, create a NEW11_mpi folder and symlink the sources directories (astest, bibc, bibfor, bibf90, bibpyt, catalo, catapy, fermetur, materiau) from NEW11_mpi to NEW11. This helps :
- saving space
- keeping both the sequential and parallel version up-to-date to the same version (this removes the need of updating both NEW11 and NEW11_mpi with auto_update, you only have to update NEW11 then build NEW11_mpi using as_run --make --vers=NEW11_mpi)

TdS

JMB365 · 2011-10-13 13:41:34

Hello TdS,
Thank you for the quick insight and all your previous timely guidance. What you recommend makes perfect sense, I will try to implement it. Regards, JMB

JMB365 · 2011-10-16 18:47:29

Thomas DE SOZA wrote:

The only thing better you can do is : instead of duplicating NEW11 to NEW11_mpi, create a NEW11_mpi folder and symlink the sources directories (astest, bibc, bibfor, bibf90, bibpyt, catalo, catapy, fermetur, materiau) from NEW11_mpi to NEW11.

Hello TdS,

I tried your advice by doing:

mv astest astest.orig
ln -s /opt/aster/NEW11.0/astest /opt/aster/NEW11.0_mpi/astest

and the like for: bib*, cata*, fermetur and materiau. This does not work for asterX_mpi as it causes a bizzare message reported on:
http://www.code-aster.org/forum2/viewtopic.php?id=15808

So for the moment I would not recommend what you have suggested. I am open to your counter argument, any mistake I have made or further examination. I come to this conclusion after having tested it both ways on Ver 11.0.10-2. I will try it out on 11.0.27 and report back.

Regards, JMB

Thomas DE SOZA · 2011-10-16 19:14:48

Hi,

Here's what I have in my NEW11_prof directory (a profiling equipped version created from the sources of my main NEW11 version) :

desoza@claut621:~$ ll /opt/aster/NEW11_prof/
total 167900
-rwxr-xr-x 1 aster aster 86489315 2011-10-12 16:01 asterd
-rwxr-xr-x 1 aster aster 60110049 2011-10-12 16:02 asteru
lrwxrwxrwx 1 aster aster       15 2011-04-20 11:27 astest -> ../NEW11/astest
-rw-r--r-- 1 aster aster      516 2011-04-06 11:23 astout.export
lrwxrwxrwx 1 aster aster       13 2011-04-20 11:27 bibc -> ../NEW11/bibc
lrwxrwxrwx 1 aster aster       15 2011-04-20 11:27 bibf90 -> ../NEW11/bibf90
lrwxrwxrwx 1 aster aster       15 2011-04-20 11:27 bibfor -> ../NEW11/bibfor
lrwxrwxrwx 1 aster aster       15 2011-04-20 11:27 bibpyt -> ../NEW11/bibpyt
-rw-r--r-- 1 aster aster  4771757 2011-10-12 16:03 cata_ele.pickled
lrwxrwxrwx 1 aster aster       15 2011-04-20 11:27 catalo -> ../NEW11/catalo
lrwxrwxrwx 1 aster aster       15 2011-04-20 11:27 catapy -> ../NEW11/catapy
drwxr-xr-x 2 aster aster     4096 2010-12-24 14:26 commande
-rw-r--r-- 1 aster aster     7192 2011-06-07 14:19 config.txt
-rw-r--r-- 1 aster aster 20480008 2011-10-12 16:03 elements
lrwxrwxrwx 1 aster aster       17 2011-04-20 11:27 fermetur -> ../NEW11/fermetur
-rw-r--r-- 1 aster aster      598 2011-04-06 11:23 forma01a.export
-rw-r--r-- 1 aster aster    18341 2010-12-07 16:32 GPL.txt
lrwxrwxrwx 1 aster aster       15 2011-04-20 11:27 histor -> ../NEW11/histor
drwxr-xr-x 2 aster aster     4096 2011-10-12 16:02 lib
-rw-r--r-- 1 aster aster      988 2010-12-07 16:32 LICENSE.TERMS
lrwxrwxrwx 1 aster aster       14 2010-12-24 13:52 Makefile -> Makefile.asrun
-rw-r--r-- 1 aster aster      714 2011-04-06 11:23 Makefile.asrun
-rw-r--r-- 1 aster aster     5775 2010-12-20 17:27 Makefile.package
lrwxrwxrwx 1 aster aster       17 2011-04-20 11:27 materiau -> ../NEW11/materiau
drwxr-xr-x 6 aster aster     4096 2010-12-24 14:25 obj
-rw-r--r-- 1 aster aster     1593 2010-12-24 14:10 profile.sh

and in the config.txt :

#
SRCFOR         | src     | 11-04 | bibfor
SRCF90         | src     | 11-04 | bibf90
SRCFERM        | src     | 11-04 | fermetur
SRCC           | src     | 11-04 | bibc
SRCPY          | src     | 11-04 | bibpyt
SRCCATA        | src     | 11-04 | catalo
SRCCAPY        | src     | 11-04 | catapy
SRCTEST        | src     | 11-04 | astest
SRCMAT         | src     | 11-04 | materiau
SRCHIST        | src     | 11-04 | histor
#
MAKE           | build   | -     | debug nodebug
BIN_NODBG      | bin     | 11-04 | asteru
BIN_DBG        | bin     | 11-04 | asterd
BINCMDE        | bin     | 11-04 | commande
BINELE         | bin     | 11-04 | elements
BINPICKLED     | bin     | 11-04 | cata_ele.pickled
BINLIB_NODBG   | bin     | 11-04 | lib/libaster.a
BINLIB_DBG     | bin     | 11-04 | lib/libasterd.a
BINLIBF_NODBG  | bin     | 02-05 | lib/libferm.a
BINLIBF_DBG    | bin     | 02-05 | lib/libfermd.a
BINOBJ_NODBG   | bin     | 11-04 | obj/aster
BINOBJF_NODBG  | bin     | 11-04 | obj/ferm
BINOBJ_DBG     | bin     | 11-04 | obj/asterd
BINOBJF_DBG    | bin     | 11-04 | obj/fermd
#
REPPY          | exec    | 11-04 | Python
ARGPYT         | exec    | 03-02 | Execution/E_SUPERV.py
ARGEXE         | exec    | 03-02 | -eficas_path ./Python
#
MAKE_SURCH_OFFI | build  | 11-04 | Lecture_Cata_Ele/make_surch_offi.py
MAKE_CAPY_OFFI  | build  | 11-04 | Lecture_Cata_Ele/make_capy_offi.py
#
REPOUT         | exec    | 11-04 | /opt/aster/outils
REPMAT         | exec    | 02-05 | /opt/aster/NEW11_prof/materiau
REPDEX         | exec    | 02-05 | /opt/aster/NEW11_prof/datg
#

TdS

JMB365 · 2011-10-18 13:40:42

Hello,

Even though I have marked this thread as solved can anybody give me a clue as to why I am getting:

--------------------------------------------------------------------------------
 Prepare cata_ele.pickled
build cata_ele.pickled with make_capy_offi.py                           [  OK  ]
<F>_PICKLED_ERROR  error during making cata_ele.pickled
--------------------------------------------------------------------------------
<F> errors previously raised :
<F>_PICKLED_ERROR  error during making cata_ele.pickled
<F>_BUILD_FAILED   Exception raised by MakeAster:
------------------------------------------------------------
Traceback:
Traceback (most recent call last):
  File "/opt/aster/lib/python2.7/site-packages/asrun/maintenance.py", line 750, in MakeAster
    _build_aster(run, conf, False, REPREF, run.get('destdir'), reptrav)
  File "/opt/aster/lib/python2.7/site-packages/asrun/maintenance.py", line 962, in _build_aster
    kret = build.MakePickled(REPREF, reptrav, repdest=destdir, **kargs)
  File "/opt/aster/lib/python2.7/site-packages/asrun/build.py", line 1170, in MakePickled
    '<F>_PICKLED_ERROR')
  File "/opt/aster/lib/python2.7/site-packages/asrun/build.py", line 156, in _mess
    self.run.Mess(msg, cod, store)
  File "/opt/aster/lib/python2.7/site-packages/asrun/run.py", line 640, in Mess
    self.Sortie(4)
  File "/opt/aster/lib/python2.7/site-packages/asrun/run.py", line 679, in Sortie
    raise RunAsterError, exit_code
RunAsterError: 4
------------------------------------------------------------
Exit code : 4

When I try my above procedures on a slower Athlon single core PC? I am trying to avoid cleaning out the /opt directory and try all over again because of the lack of speed on this test PC. Thanks

Regards, JMB

#1 2011-10-12 14:02:26

[Solved] Compile 11.0.10-2 w/ MPI, mumps & scotch (Ubuntu 11.04 64bit)

#2 2011-10-12 14:10:56

Re: [Solved] Compile 11.0.10-2 w/ MPI, mumps & scotch (Ubuntu 11.04 64bit)

#3 2011-10-12 14:40:59

Re: [Solved] Compile 11.0.10-2 w/ MPI, mumps & scotch (Ubuntu 11.04 64bit)

#4 2011-10-12 14:48:20

Re: [Solved] Compile 11.0.10-2 w/ MPI, mumps & scotch (Ubuntu 11.04 64bit)

#5 2011-10-12 15:14:30

Re: [Solved] Compile 11.0.10-2 w/ MPI, mumps & scotch (Ubuntu 11.04 64bit)

#6 2011-10-12 19:47:52

Re: [Solved] Compile 11.0.10-2 w/ MPI, mumps & scotch (Ubuntu 11.04 64bit)

#7 2011-10-12 20:34:09

Re: [Solved] Compile 11.0.10-2 w/ MPI, mumps & scotch (Ubuntu 11.04 64bit)

#8 2011-10-13 00:05:02

Re: [Solved] Compile 11.0.10-2 w/ MPI, mumps & scotch (Ubuntu 11.04 64bit)

#9 2011-10-13 02:24:38

Re: [Solved] Compile 11.0.10-2 w/ MPI, mumps & scotch (Ubuntu 11.04 64bit)

#10 2011-10-13 08:54:18

Re: [Solved] Compile 11.0.10-2 w/ MPI, mumps & scotch (Ubuntu 11.04 64bit)

#11 2011-10-13 13:41:34

Re: [Solved] Compile 11.0.10-2 w/ MPI, mumps & scotch (Ubuntu 11.04 64bit)

#12 2011-10-16 18:47:29

Re: [Solved] Compile 11.0.10-2 w/ MPI, mumps & scotch (Ubuntu 11.04 64bit)

#13 2011-10-16 19:14:48

Re: [Solved] Compile 11.0.10-2 w/ MPI, mumps & scotch (Ubuntu 11.04 64bit)

#14 2011-10-18 13:40:42

Re: [Solved] Compile 11.0.10-2 w/ MPI, mumps & scotch (Ubuntu 11.04 64bit)

Board footer