[MOAB-dev] [Nek5000-users] MOAB partitioning

Popov, Emilian L. popove at ornl.gov
Wed Nov 11 10:33:46 CST 2015 

Yes, I think I am, no hdf5. I read somewhere that it is not needed, should I add it?

Thanks,
-emilian


-----Original Message-----
From: Grindeanu, Iulian R. [mailto:iulian at mcs.anl.gov] 
Sent: Wednesday, November 11, 2015 11:32 AM
To: Popov, Emilian L.; Vijay S. Mahadevan
Cc: moab-dev at mcs.anl.gov
Subject: RE: [MOAB-dev] [Nek5000-users] MOAB partitioning

your config file says this:

  $ ./configure --prefix=/home/owp/MOAB --with-netcdf=/home/owp/netCDF --with-metis=/home/owp/METIS/metis-5.1.0

This means you are configuring without hdf5 ________________________________________
From: moab-dev-bounces at mcs.anl.gov [moab-dev-bounces at mcs.anl.gov] on behalf of Grindeanu, Iulian R. [iulian at mcs.anl.gov]
Sent: Wednesday, November 11, 2015 10:30 AM
To: Popov, Emilian L.; Vijay S. Mahadevan
Cc: moab-dev at mcs.anl.gov
Subject: Re: [MOAB-dev] [Nek5000-users] MOAB partitioning

So in one of your config files you sent earlier, you had this:

config.status:1747: executing src/MOAB_FCDefs.h commands
configure:39414: result: C:   gcc  -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align  -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG
configure:39416: result: C++: g++  -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align  -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG
configure:39419: result: Fortran90: gfortran   -O2 -lstdc++ -fcray-pointer
configure:39423: result: Fortran77: gfortran   -O2 -lstdc++ -fcray-pointer
configure:39432: WARNING:
*************************************************************************
*            MOAB has been configured w/out the HDF5 library.
*              Support for native file format is disabled!
*************************************************************************


We need to find out why
________________________________________
From: moab-dev-bounces at mcs.anl.gov [moab-dev-bounces at mcs.anl.gov] on behalf of Grindeanu, Iulian R. [iulian at mcs.anl.gov]
Sent: Wednesday, November 11, 2015 10:28 AM
To: Popov, Emilian L.; Vijay S. Mahadevan
Cc: moab-dev at mcs.anl.gov
Subject: Re: [MOAB-dev] [Nek5000-users] MOAB partitioning

so that means that your moab/hdf5 build is not fine.
does make check work everywhere?
can I see your config.log from moab ?

________________________________________
From: Popov, Emilian L. [popove at ornl.gov]
Sent: Wednesday, November 11, 2015 10:25 AM
To: Grindeanu, Iulian R.; Vijay S. Mahadevan
Cc: moab-dev at mcs.anl.gov
Subject: RE: [MOAB-dev] [Nek5000-users] MOAB partitioning

I converted it with 'mbconvert from an exodus file

Thanks,
-emilian


-----Original Message-----
From: Grindeanu, Iulian R. [mailto:iulian at mcs.anl.gov]
Sent: Wednesday, November 11, 2015 11:22 AM
To: Popov, Emilian L.; Vijay S. Mahadevan
Cc: moab-dev at mcs.anl.gov
Subject: RE: [MOAB-dev] [Nek5000-users] MOAB partitioning

It is not an h5m file, it is exodus
so I assume the h5m moab writer failed, and used exodus writer

how did you get this file?
if you change the extension to exo,
(pipe150cm.exo)
it will work

with something like
mbpart -m ML_KWAY 32 pipe150cm.exo  out.h5m

Still, how did you obtain it?

Thanks,
Iulian

________________________________________
From: moab-dev-bounces at mcs.anl.gov [moab-dev-bounces at mcs.anl.gov] on behalf of Popov, Emilian L. [popove at ornl.gov]
Sent: Wednesday, November 11, 2015 10:12 AM
To: Vijay S. Mahadevan
Cc: moab-dev at mcs.anl.gov
Subject: Re: [MOAB-dev] [Nek5000-users] MOAB partitioning

The check on Moab build passes with no error messages: I don't know how to run Metis programs, but run one of them with help option and it displays the help, so I suppose I can run them.

Here is the mesh file I use:

Thanks,
-emilian


-----Original Message-----
From: Vijay S. Mahadevan [mailto:vijay.m at gmail.com]
Sent: Wednesday, November 11, 2015 10:39 AM
To: Popov, Emilian L.
Cc: moab-dev at mcs.anl.gov
Subject: Re: [MOAB-dev] [Nek5000-users] MOAB partitioning

Did make check pass on your MOAB build ? Can you run the programs in metis bin directory ?

If the answer is yes to both questions above, can you send us the mesh file (hopefully not too large) that needs to be partitioned so that we can see if this is replicable ?

Vijay


On Wed, Nov 11, 2015 at 9:32 AM, Popov, Emilian L. <popove at ornl.gov> wrote:
> Vijay and all:
>
> When I run: mbpart -m ML_KWAY 32  <file> the code exits with a segmentation fault. Any thoughts?
>
> Thanks,
> -emilian
>
>
> -----Original Message-----
> From: Vijay S. Mahadevan [mailto:vijay.m at gmail.com]
> Sent: Monday, November 09, 2015 10:27 AM
> To: Popov, Emilian L.
> Subject: Re: [MOAB-dev] [Nek5000-users] MOAB partitioning
>
> You can run "make check" to verify the build worked fine. Then run "make install", go to build/examples directory, use the makefile to compile an example. Update MOAB_DIR as needed in the makefile.
>
> Let us know if you run into any other issues.
>
> Vijay
>
> On Mon, Nov 9, 2015 at 9:21 AM, Popov, Emilian L. <popove at ornl.gov> wrote:
>> Yes, that was the problem, all looks OK now, appreciate the help. Moab seems to install fine as well. Is there any way I can test the Moab install?
>>
>> Thanks,
>> -emilian
>>
>>
>> -----Original Message-----
>> From: Vijay S. Mahadevan [mailto:vijay.m at gmail.com]
>> Sent: Monday, November 09, 2015 10:11 AM
>> To: Popov, Emilian L.; moab-dev at mcs.anl.gov
>> Subject: Re: [MOAB-dev] [Nek5000-users] MOAB partitioning
>>
>> You need to install metis (make install). This will install the header/libs under the prefix directory if you specified it during configuration.
>>
>> MOAB will NOT work with Metis source directory. Let me know if your installation went correctly.
>>
>> Vijay
>>
>> On Mon, Nov 9, 2015 at 9:06 AM, Popov, Emilian L. <popove at ornl.gov> wrote:
>>> Hi Vijay,
>>> I rebuilt metis, and it should be fine now. The library 'libmetis.a' is in ..../metis-5.1.0/build/Linux-x86_64/libmetis, there is no /lib directory.
>>> Let me know pls whether I need to change the Moab configure script in one way or other.
>>>
>>> Thanks,
>>> -emilian
>>>
>>> -----Original Message-----
>>> From: Vijay S. Mahadevan [mailto:vijay.m at gmail.com]
>>> Sent: Thursday, November 05, 2015 5:42 PM
>>> To: Popov, Emilian L.
>>> Subject: Re: [MOAB-dev] [Nek5000-users] MOAB partitioning
>>>
>>> Hmm, I would say that your installation is screwed up for metis. Are you sure you configured Metis with a prefix ? MOAB can only work with the installed metis directory and not directly with the sources since these keep changing every version.
>>>
>>> When you install Metis correctly, you should see something like this:
>>>
>>> [ vijaysm at tachyon ~  ]> find /usr/software/metis-5.1.0/ 
>>> /usr/software/metis-5.1.0/ /usr/software/metis-5.1.0/include 
>>> /usr/software/metis-5.1.0/include/metis.h
>>> /usr/software/metis-5.1.0/bin
>>> /usr/software/metis-5.1.0/bin/cmpfillin
>>> /usr/software/metis-5.1.0/bin/ndmetis
>>> /usr/software/metis-5.1.0/bin/graphchk
>>> /usr/software/metis-5.1.0/bin/m2gmetis
>>> /usr/software/metis-5.1.0/bin/gpmetis
>>> /usr/software/metis-5.1.0/bin/mpmetis
>>> /usr/software/metis-5.1.0/lib
>>> /usr/software/metis-5.1.0/lib/libmetis.a
>>>
>>> Vijay
>>>
>>> On Thu, Nov 5, 2015 at 4:34 PM, Popov, Emilian L. <popove at ornl.gov> wrote:
>>>> I'm not sure whether we look for a dynamic/static library or for bunch of files, but in /home/owp/METIS/metis-5.1.0 there is a folder 'libmetis' that contains several C files and headers.
>>>>
>>>> Thanks,
>>>> -emilian
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: Vijay S. Mahadevan [mailto:vijay.m at gmail.com]
>>>> Sent: Thursday, November 05, 2015 5:03 PM
>>>> To: Popov, Emilian L.
>>>> Subject: Re: [MOAB-dev] [Nek5000-users] MOAB partitioning
>>>>
>>>> From your config.log
>>>>
>>>> METIS_INC_FLAGS='-I/home/owp/METIS/metis-5.1.0/include'
>>>> METIS_LIBS='-L/home/owp/METIS/metis-5.1.0 -lmetis'
>>>>
>>>> Is the metis library not in /home/owp/METIS/metis-5.1.0 ? Is it in /home/owp/METIS/metis-5.1.0/lib ? Please verify and let me know. It configures fine on my local build and on our nightlies.
>>>>
>>>> Vijay
>>>>
>>>> On Thu, Nov 5, 2015 at 2:51 PM, Popov, Emilian L. <popove at ornl.gov> wrote:
>>>>> See the end of make.log: from the patched version
>>>>>
>>>>> Thanks,
>>>>> -emilian
>>>>>
>>>>>
>>>>> -----Original Message-----
>>>>> From: Vijay S. Mahadevan [mailto:vijay.m at gmail.com]
>>>>> Sent: Thursday, November 05, 2015 3:33 PM
>>>>> To: Popov, Emilian L.; moab-dev at mcs.anl.gov
>>>>> Subject: Re: [MOAB-dev] [Nek5000-users] MOAB partitioning
>>>>>
>>>>> If you are still interested in a patched tarball, its available at
>>>>>
>>>>> ftp://ftp.mcs.anl.gov/pub/fathom/moab-4.8.2p1.tar.gz
>>>>>
>>>>> Let me know if this fixes your issues. Thanks.
>>>>>
>>>>> Vijay
>>>>>
>>>>> On Thu, Nov 5, 2015 at 2:27 PM, Vijay S. Mahadevan <vijay.m at gmail.com> wrote:
>>>>>> Ah I see. I recently merge a PR to fix precisely this issue.
>>>>>>
>>>>>> https://bitbucket.org/fathomteam/moab/pull-requests/157/fix-metis
>>>>>> -
>>>>>> p
>>>>>> a
>>>>>> r
>>>>>> t
>>>>>> itioner-for-serial-builds/diff
>>>>>>
>>>>>> I can backport the fix to moab-4.8.2 if you prefer that. Or you 
>>>>>> could directly use MOAB master from Bitbucket 
>>>>>> (https://bitbucket.org/fathomteam/moab/overview).
>>>>>>
>>>>>> Vijay
>>>>>>
>>>>>> On Thu, Nov 5, 2015 at 2:00 PM, Popov, Emilian L. <popove at ornl.gov> wrote:
>>>>>>> Apparently I've sent you the config log instead of make log. Here it is, complains form 'mpi.h'
>>>>>>>
>>>>>>> Thanks,
>>>>>>> -emilian
>>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: Vijay S. Mahadevan [mailto:vijay.m at gmail.com]
>>>>>>> Sent: Thursday, November 05, 2015 12:49 PM
>>>>>>> To: Popov, Emilian L.
>>>>>>> Cc: moab-dev at mcs.anl.gov
>>>>>>> Subject: Re: [MOAB-dev] [Nek5000-users] MOAB partitioning
>>>>>>>
>>>>>>> Emilian, I don't see what is the problem anymore. MOAB successfully configured according to your logs and mbpart will be built with Metis support. From your output:
>>>>>>>
>>>>>>> METIS_INC_FLAGS='-I/home/owp/METIS/metis-5.1.0/include'
>>>>>>> METIS_LIBS='-L/home/owp/METIS/metis-5.1.0 -lmetis'
>>>>>>> #define HAVE_METIS 1
>>>>>>>
>>>>>>> So I don't see any issues here. Send us the error output from make ?
>>>>>>>
>>>>>>> Vijay
>>>>>>>
>>>>>>> On Thu, Nov 5, 2015 at 11:39 AM, Popov, Emilian L. <popove at ornl.gov> wrote:
>>>>>>>> Hello Vijay,
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Is there any resolution on the below.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> -emilian
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> From: nek5000-users-bounces at lists.mcs.anl.gov
>>>>>>>> [mailto:nek5000-users-bounces at lists.mcs.anl.gov] On Behalf Of 
>>>>>>>> nek5000-users at lists.mcs.anl.gov
>>>>>>>> Sent: Tuesday, October 27, 2015 2:59 PM
>>>>>>>> To: nek5000-users at lists.mcs.anl.gov; moab-dev at mcs.anl.gov
>>>>>>>>
>>>>>>>> Subject: Re: [Nek5000-users] MOAB partitioning
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Emilian,
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Let's fix the MOAB related issues first on the MOAB mailing list.
>>>>>>>> Please send us your config.log file so that we can provide 
>>>>>>>> pointers to fix the configuration problems. Once this is done, we can revisit NEK-MOAB.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Vijay
>>>>>>>>
>>>>>>>> On Monday, October 26, 2015, <nek5000-users at lists.mcs.anl.gov> wrote:
>>>>>>>>
>>>>>>>> Vijay,
>>>>>>>>
>>>>>>>> I downloaded moab-4.8.2 and configured and then ran 'make', but 
>>>>>>>> am getting errors from missing 'mpi.h' and metis.h, perhaps the 
>>>>>>>> configuration is not OK?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> -emilian
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> From: nek5000-users-bounces at lists.mcs.anl.gov
>>>>>>>> [mailto:nek5000-users-bounces at lists.mcs.anl.gov] On Behalf Of 
>>>>>>>> nek5000-users at lists.mcs.anl.gov
>>>>>>>> Sent: Friday, October 23, 2015 12:24 PM
>>>>>>>> To: nek5000-users at lists.mcs.anl.gov
>>>>>>>> Subject: Re: [Nek5000-users] MOAB partitioning
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> What version of MOAB are you using ? It should be available 
>>>>>>>> with the last MOAB 4.8.2 release [1] I think. Let us know if you have problems.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Vijay
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> [1] http://ftp.mcs.anl.gov/pub/fathom/moab-4.8.2.tar.gz
>>>>>>>>
>>>>>>>>
>>>>>>>> On Friday, October 23, 2015, <nek5000-users at lists.mcs.anl.gov> wrote:
>>>>>>>>
>>>>>>>> Thanks Vijay, however the option '-with-metis' does not seem to 
>>>>>>>> exist, please advice.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> -emilian
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> From: nek5000-users-bounces at lists.mcs.anl.gov
>>>>>>>> [mailto:nek5000-users-bounces at lists.mcs.anl.gov] On Behalf Of 
>>>>>>>> nek5000-users at lists.mcs.anl.gov
>>>>>>>> Sent: Friday, October 23, 2015 11:35 AM
>>>>>>>> To: nek5000-users at lists.mcs.anl.gov
>>>>>>>> Subject: Re: [Nek5000-users] MOAB partitioning
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Emilian,
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> If you want the partitioner tools, you need to configure MOAB 
>>>>>>>> with either metis (--with-metis=DIR) or with zoltan and 
>>>>>>>> optionally parmetis. Let us know if you have questions. The 
>>>>>>>> metis installation route is extremely straightforward and you should not encounter any issues.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Vijay
>>>>>>>>
>>>>>>>> On Friday, October 23, 2015, <nek5000-users at lists.mcs.anl.gov> wrote:
>>>>>>>>
>>>>>>>> Dear Nek/Moab users,
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> I built Moab, but in the bin folder the 'mbpart' code is 
>>>>>>>> missing and I need it to partition an .h5m mesh file for Nek.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Any suggestions?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> -emilian
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>
>>>>
>>>
>>
>

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