[gmx-users] EXTERNAL: Re: gromacs make check failure
Paul bauer
paul.bauer.q at gmail.com
Mon May 20 18:26:40 CEST 2019
Hello,
if it takes this long then something is going wrong, so you don't need
to wait that long.
What happens when you build without MPI?
Cheers
Paul
On 20/05/2019 18:14, Nelson Chris AWE wrote:
> Thanks Paul,
> I have run the binary manually, and it's been going for over an hour now so I guess there is something wrong with it - I'll leave it running overnight and see if it completes.
> Cheers,
> Chris
>
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Paul bauer
> Sent: 20 May 2019 15:34
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: EXTERNAL: Re: [gmx-users] gromacs make check failure
>
> Hello,
>
> from looking at the output from make check it looks like this is harmless. The tests simply took longer than the internally set cut-off of 30 seconds.
> If you are unsure about the build, you can run the test binary manually from the build directory with (./gmxpreprocess-test in the same directory where you can find the gmx binary).
> Then it won't use the cut-off and will take as much time as it will need.
>
> Cheers
>
> Paul
>
> On 20/05/2019 16:26, Nelson Chris AWE wrote:
>> Hi All,
>> I've built gromacs on an Intel x86_64 server with GCC 7.2.0 and
>> OpenMPI
>>
>> When I run make check, I get a failure on test 29:
>>
>> 29 - GmxPreprocessTests (Timeout)
>>
>> Any advice would be much appreciated.
>>
>> Links to output files:
>>
>> 1. Build environment (https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fopen%3Fid%3D1tBs6scDqR_gJLtBRzpxMSEdbWwxYR5ks&data=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0&sdata=vq67KLEfO8%2FOvDEx80mS22FpO4B4WogQbKHS5UKEO%2Bk%3D&reserved=0 )
>> 2. Build output (https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fopen%3Fid%3D1PQFllv49M-Op6HLtdKsRJfwHbFeEsint&data=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0&sdata=kvDO4%2FnuLOUAz2SemHqGQ2XuN%2Fdzbwz%2B9S4bk%2BAFsfs%3D&reserved=0 )
>> 3. Dependency list (https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fopen%3Fid%3D13rETIX_ejMs1DPBGcTdsQfWKeYFNwd7T&data=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0&sdata=ckVLYxFG0XpM797geks%2Fpmd75B5SSDt8EZt8J0Aro5w%3D&reserved=0 )
>> 4. Make checkout output (https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fopen%3Fid%3D1YpAEbPSj0eEe2JERbL6OIc49Gd5e57a1&data=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0&sdata=ylFHabQdXHeSBIQ4TNhujWeRin5jTkKFv7VAhuCmzR8%3D&reserved=0 )
>> 5. mdrun - version output
>> (https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdri
>> ve.google.com%2Fopen%3Fid%3D1qu44Mk_aLz3d65YldDKo5mMtvJVyvb6D&data
>> =01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9
>> %7C72654b74be024361a62716b132e3fdd0%7C0&sdata=UIVAn%2BTTdZx6ljvGQl
>> %2FQA4jJM1A%2Bbz3dvK8YmGAoBd8%3D&reserved=0 )
>>
>> Kind regards,
>> Chris.
>>
>>
>> Christopher J. Nelson
>> High Performance Computing
>> Direct: +44(0)118 98 55021
>> F161.1, AWE, Aldermaston, Reading, RG7 4PR, UK
>>
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>
> --
> Paul Bauer, PhD
> GROMACS Release Manager
> KTH Stockholm, SciLifeLab
> 0046737308594
>
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Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594
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