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

Mon Nov 9 09:10:54 CST 2015

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-pa
>>>> 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
>>>>>>
>>>>>>
>>>>>
>>>
>>
>