Hi Paul, If I build without MPI, all tests complete successfully. 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 17:27 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] EXTERNAL: Re: gromacs make check failure 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%7Cc281092a0d434d6a1ca408d6dd400260%7C72654b74be024361a62716b132e3fdd0%7C0&sdata=XRtHd3%2FNwAlX04vziL9aQnBvX2xF8v0m%2Fn3vXeG4yFg%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%7Cc281092a0d434d6a1ca408d6dd400260%7C72654b74be024361a62716b132e3fdd0%7C0&sdata=Ypjb%2BqqeKwSZKMr7NfYJppG8j1xIkf%2BPv%2Fp06RjY9KQ%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%7Cc281092a0d434d6a1ca408d6dd400260%7C72654b74be024361a62716b132e3fdd0%7C0&sdata=1SvraolwP90kbFWYwmX1k0nTHjgoBg7cx9NBosnZ43M%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%7Cc281092a0d434d6a1ca408d6dd400260%7C72654b74be024361a62716b132e3fdd0%7C0&sdata=hIUzlrZ4cVMTCVwCOWUul4HJ7lNpH8v9EspptFO47C8%3D&reserved=0 >> ) >> 5. mdrun - version output >> (https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdr >> i >> ve.google.com%2Fopen%3Fid%3D1qu44Mk_aLz3d65YldDKo5mMtvJVyvb6D&dat >> a >> =01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f >> 9 >> %7C72654b74be024361a62716b132e3fdd0%7C0&sdata=UIVAn%2BTTdZx6ljvGQ >> l >> %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 >> >> The information in this email and in any attachment(s) is commercial >> in confidence. If you are not the named addressee(s) or if you >> receive this email in error then any distribution, copying or use of >> this communication or the information in it is strictly prohibited. >> Please notify us immediately by email at admin.internet(at)awe.co.uk, >> and then delete this message from your computer. While attachments >> are virus checked, AWE plc does not accept any liability in respect >> of any virus which is not detected. AWE Plc Registered in England and >> Wales Registration No 02763902 AWE, Aldermaston, Reading, RG7 4PR > > -- > Paul Bauer, PhD > GROMACS Release Manager > KTH Stockholm, SciLifeLab > 0046737308594 > > -- > Gromacs Users mailing list > > * Please search the archive at > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&data=01%7C01%7Cchris.nelson%40awe.co.uk%7Cc281092a0d434d6a1ca408d6dd400260%7C72654b74be024361a62716b132e3fdd0%7C0&sdata=1yEf9xf1ZmlYBNBRwP5ubLGAXdBsREUnEy1HodNLdnE%3D&reserved=0 > before posting! > > * Can't post? Read > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.g > romacs.org%2FSupport%2FMailing_Lists&data=01%7C01%7Cchris.nelson%4 > 0awe.co.uk%7Cc281092a0d434d6a1ca408d6dd400260%7C72654b74be024361a62716 > b132e3fdd0%7C0&sdata=YcK7M2Czecl%2BykPooJhw9i3yx2fmNpneScihrKEzyqA > %3D&reserved=0 > > * For (un)subscribe requests visit > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users&data=01%7C01%7Cchris.nelson%40awe.co.uk%7Cc281092a0d434d6a1ca408d6dd400260%7C72654b74be024361a62716b132e3fdd0%7C0&sdata=104s828Dp5q99ssFsXmUCsx5qT%2BB16L%2BYPnFsOxDGrw%3D&reserved=0 > or send a mail to gmx-users-requ...@gromacs.org. > The information in this email and in any attachment(s) is commercial > in confidence. If you are not the named addressee(s) or if you receive > this email in error then any distribution, copying or use of this > communication or the information in it is strictly prohibited. Please > notify us immediately by email at admin.internet(at)awe.co.uk, and > then delete this message from your computer. While attachments are > virus checked, AWE plc does not accept any liability in respect of any > virus which is not detected. AWE Plc Registered in England and Wales > Registration No 02763902 AWE, Aldermaston, Reading, RG7 4PR -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- Gromacs Users mailing list * Please search the archive at https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&data=01%7C01%7Cchris.nelson%40awe.co.uk%7Cc281092a0d434d6a1ca408d6dd400260%7C72654b74be024361a62716b132e3fdd0%7C0&sdata=1yEf9xf1ZmlYBNBRwP5ubLGAXdBsREUnEy1HodNLdnE%3D&reserved=0 before posting! * Can't post? Read https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&data=01%7C01%7Cchris.nelson%40awe.co.uk%7Cc281092a0d434d6a1ca408d6dd400260%7C72654b74be024361a62716b132e3fdd0%7C0&sdata=YcK7M2Czecl%2BykPooJhw9i3yx2fmNpneScihrKEzyqA%3D&reserved=0 * For (un)subscribe requests visit https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users&data=01%7C01%7Cchris.nelson%40awe.co.uk%7Cc281092a0d434d6a1ca408d6dd400260%7C72654b74be024361a62716b132e3fdd0%7C0&sdata=104s828Dp5q99ssFsXmUCsx5qT%2BB16L%2BYPnFsOxDGrw%3D&reserved=0 or send a mail to gmx-users-requ...@gromacs.org. The information in this email and in any attachment(s) is commercial in confidence. If you are not the named addressee(s) or if you receive this email in error then any distribution, copying or use of this communication or the information in it is strictly prohibited. Please notify us immediately by email at admin.internet(at)awe.co.uk, and then delete this message from your computer. While attachments are virus checked, AWE plc does not accept any liability in respect of any virus which is not detected. AWE Plc Registered in England and Wales Registration No 02763902 AWE, Aldermaston, Reading, RG7 4PR -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
