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

Wed Nov 11 09:32:15 CST 2015

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
>>>>>>>
>>>>>>>
>>>>>>
>>>>
>>>
>>
>