Re: [petsc-users] Could not execute "['git', 'rev-parse', '--git-dir']"
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 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 > 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 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 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 >>> > 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 >>>>> 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 >>>>>> 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
Re: [petsc-users] Could not execute "['git', 'rev-parse', '--git-dir']"
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 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 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
>> 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 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 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
>>>>> 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=WF6ZxIh9Z9Hh2kYY0w70aNrgfPicp6
>>>>> > > 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
Re: [petsc-users] Could not execute "['git', 'rev-parse', '--git-dir']"
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 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 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:des
>> ktop-4.0-noarch:graphics-2.0-amd64:graphics-2.0-noarch:grap
>> hics-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 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=WF6ZxIh9Z9Hh2kYY0w70aNrgfPicp6
>> > > 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
