[petsc-users] Could not execute "['git', 'rev-parse', '--git-dir']"

Thu Apr 5 12:21:35 CDT 2018

I made some changes to the falcon cluster environment. Please try the
default git (i.e Without loading a module) and
see if petsc will install correctly.

Thanks,
Cormac.

On Wed, Apr 4, 2018 at 5:09 PM, Fande Kong <fdkong.jd at gmail.com> wrote:

> The default git gives me:
>
> *Could not execute "['git', 'rev-parse', '--git-dir']"*
>
> when I am configuring PETSc.
>
> The manually loaded *gits*  work just fine.
>
>
> Fande,
>
>
> On Wed, Apr 4, 2018 at 5:04 PM, Garvey, Cormac T <cormac.garvey at inl.gov>
> wrote:
>
>> I though it was fixed, yes I will look into it again.
>>
>> Do you get an error just doing a git clone on falcon1 and falcon2?
>>
>> On Wed, Apr 4, 2018 at 4:48 PM, Kong, Fande <fande.kong at inl.gov> wrote:
>>
>>> module load git/2.16.2-GCCcore-5.4.0"  also works.
>>>
>>> Could you somehow make the default git work as well? Hence we do not
>>> need to have this extra "module load for git"
>>>
>>> Fande,
>>>
>>> On Wed, Apr 4, 2018 at 4:43 PM, Kong, Fande <fande.kong at inl.gov> wrote:
>>>
>>>> Thanks, Cormac,
>>>>
>>>> *module load git/1.8.5.2-GCC-4.8.3 *
>>>>
>>>> works for me.
>>>>
>>>> Did not try "module load git/2.16.2-GCCcore-5.4.0" yet.
>>>>
>>>> I will try, and get it back here.
>>>>
>>>>
>>>>
>>>> Fande
>>>>
>>>> On Wed, Apr 4, 2018 at 4:39 PM, Garvey, Cormac T <cormac.garvey at inl.gov
>>>> > wrote:
>>>>
>>>>>
>>>>> We needed to rebuilt git on the INL falcon cluster because github
>>>>> server changed such that it no longer accepted TLSv1.
>>>>>
>>>>> The default git on the falcon cluster /usr/bin/git is just a wrapper
>>>>> script, so users would not need to load any modules to
>>>>> use git.
>>>>>
>>>>> When you load load git on falcon1 or falcon2 does it still fail?
>>>>>
>>>>> module load git/2.16.2-GCCcore-5.4.0
>>>>>
>>>>> Thanks,
>>>>> Cormac.
>>>>>
>>>>>
>>>>>
>>>>> On Wed, Apr 4, 2018 at 4:28 PM, Kong, Fande <fande.kong at inl.gov>
>>>>> wrote:
>>>>>
>>>>>> Hi Cormac,
>>>>>>
>>>>>> Do you know anything on "git"? How did you guys build git on the
>>>>>> falcon1?  The default git on Falcon1 does not work with petsc any more.
>>>>>>
>>>>>>
>>>>>> Fande,
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Wed, Apr 4, 2018 at 4:20 PM, Satish Balay <balay at mcs.anl.gov>
>>>>>> wrote:
>>>>>>
>>>>>>> Ok - I don't think I have access to this OS.
>>>>>>>
>>>>>>> And I see its from 2009 [sure its enterprise os - with regular
>>>>>>> backport updates]
>>>>>>>
>>>>>>> But its wierd that you have such a new version of git at /usr/bin/git
>>>>>>>
>>>>>>> From what we know so far - the problem appears to be some bad
>>>>>>> interaction of python-2.6 with this old OS [i.e old glibc etc..] -
>>>>>>> and
>>>>>>> this new git version [binary built locally or on a different OS and
>>>>>>> installed locally ?].
>>>>>>>
>>>>>>> Satish
>>>>>>>
>>>>>>> On Wed, 4 Apr 2018, Kong, Fande wrote:
>>>>>>>
>>>>>>> >  moose]$ uname -a
>>>>>>> > Linux falcon1 3.0.101-108.13-default #1 SMP Wed Oct 11 12:30:40
>>>>>>> UTC 2017
>>>>>>> > (294ccfe) x86_64 x86_64 x86_64 GNU/Linux
>>>>>>> >
>>>>>>> >
>>>>>>> > moose]$ lsb_release -a
>>>>>>> > LSB Version:
>>>>>>> > core-2.0-noarch:core-3.2-noarch:core-4.0-noarch:core-2.0-x86
>>>>>>> _64:core-3.2-x86_64:core-4.0-x86_64:desktop-4.0-amd64:deskto
>>>>>>> p-4.0-noarch:graphics-2.0-amd64:graphics-2.0-noarch:graphics
>>>>>>> -3.2-amd64:graphics-3.2-noarch:graphics-4.0-amd64:graphics-4
>>>>>>> .0-noarch
>>>>>>> > Distributor ID:    SUSE LINUX
>>>>>>> > Description:    SUSE Linux Enterprise Server 11 (x86_64)
>>>>>>> > Release:    11
>>>>>>> > Codename:    n/a
>>>>>>> >
>>>>>>> >
>>>>>>> >
>>>>>>> > On Wed, Apr 4, 2018 at 4:08 PM, Satish Balay <balay at mcs.anl.gov>
>>>>>>> wrote:
>>>>>>> >
>>>>>>> > > On Wed, 4 Apr 2018, Satish Balay wrote:
>>>>>>> > >
>>>>>>> > > > On Wed, 4 Apr 2018, Satish Balay wrote:
>>>>>>> > > >
>>>>>>> > > > > was your '2.16.2' version installed from source?
>>>>>>> > > >
>>>>>>> > > > >>>
>>>>>>> > > > Checking for program /usr/bin/git...found
>>>>>>> > > >                 Defined make macro "GIT" to "git"
>>>>>>> > > > Executing: git --version
>>>>>>> > > > stdout: git version 2.16.2
>>>>>>> > > > <<<<
>>>>>>> > > >
>>>>>>> > > > I gues its the OS default package
>>>>>>> > > >
>>>>>>> > > > >>>>>
>>>>>>> > > > Machine platform:
>>>>>>> > > > ('Linux', 'falcon1', '3.0.101-108.13-default', '#1 SMP Wed Oct
>>>>>>> 11
>>>>>>> > > 12:30:40 UTC 2017 (294ccfe)', 'x86_64', 'x86_64')
>>>>>>> > > > Python version:
>>>>>>> > > > 2.6.9 (unknown, Aug  5 2016, 11:15:31)
>>>>>>> > > > [GCC 4.3.4 [gcc-4_3-branch revision 152973]]
>>>>>>> > > > <<<<
>>>>>>> > > >
>>>>>>> > > > What OS/version is on this machine? I can try reproducing in a
>>>>>>> VM
>>>>>>> > >
>>>>>>> > > It is strange that the kernel is old [3.0 - perhaps LTS OS] ,
>>>>>>> python is
>>>>>>> > > old [2.6] - but git is new? [2.16?]
>>>>>>> > >
>>>>>>> > > https://urldefense.proofpoint.com/v2/url?u=https-3A__
>>>>>>> > > mirrors.edge.kernel.org_pub_software_scm_git_&d=DwIBAg&c=
>>>>>>> > > 54IZrppPQZKX9mLzcGdPfFD1hxrcB__aEkJFOKJFd00&r=DUUt3SRGI0_
>>>>>>> > > JgtNaS3udV68GRkgV4ts7XKfj2opmiCY&m=WF6ZxIh9Z9Hh2kYY0w70aNrgf
>>>>>>> Picp6
>>>>>>> > > kgIh5BvezPiEY&s=KWMsO7XC0-pQuQ_mD03tNJWEpxSTATlZW_DmX0QofGw&e=
>>>>>>> > > git-2.16.2.tar.gz                                  16-Feb-2018
>>>>>>> 17:48
>>>>>>> > > 7M
>>>>>>> > >
>>>>>>> > > Satish
>>>>>>> > >
>>>>>>> >
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Cormac Garvey
>>>>> HPC Software Consultant
>>>>> Scientific Computing
>>>>> Idaho National Laboratory
>>>>> Ph: 208-526-6294
>>>>>
>>>>>
>>>>
>>>
>>
>>
>> --
>> Cormac Garvey
>> HPC Software Consultant
>> Scientific Computing
>> Idaho National Laboratory
>> Ph: 208-526-6294
>>
>>
>

-- 
Cormac Garvey
HPC Software Consultant
Scientific Computing
Idaho National Laboratory
Ph: 208-526-6294
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