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-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of Paul bauer
Sent: 20 May 2019 15:34
To: gromacs.org_gmx-users@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
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