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

Thu Apr 5 13:47:04 CDT 2018

Hi Cormac,

Thanks so much! It is working now.

Fande,

On Thu, Apr 5, 2018 at 11:21 AM, Garvey, Cormac T <cormac.garvey at inl.gov>
wrote:

> 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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