Re: [gmx-users] EXTERNAL: Re: gromacs make check failure
Thanks for the clarification Paul. Cheers, Chris. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Paul bauer Sent: 21 May 2019 16:00 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] EXTERNAL: Re: gromacs make check failure Hello Chris, in this case I think everything is fine with your build. As you can see from the MPI build log it is only the test harness complaining and nothing more. Happy simulations! Cheers Paul On 21/05/2019 16:00, Nelson Chris AWE wrote: > 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 > 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 >> 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%7C5778fed201e443882e1308d6ddfd29e9%7C72654b74be024361a62716b132e3fdd0%7C0&sdata=GsHvflQw3RgyzNr1%2FC6jghqfRpYkaXH5yua8Q4gsSiE%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%7C5778fed201e443882e1308d6ddfd29e9%7C72654b74be024361a62716b132e3fdd0%7C0&sdata=5s70TQsKP2eAxWGivwdYiDwP%2BSeK2XiLFRQyuUitCic%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%7C5778fed201e443882e1308d6ddfd29e9%7C72654b74be024361a62716b132e3fdd0%7C0&sdata=Molg%2FMQygtJ21bHGCRIylKUPe7xkGtOPusid3lNmlsQ%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%7C5778fed201e443882e1308d6ddfd29e9%7C72654b74be024361a62716b132e3fdd0%7C0&sdata=RutZ%2FKkvfh%2FSDCavbPt2Tu0t9XQz0X7ouMHaS2SeieE%3D&reserved=0 >>> ) >>> 5. mdrun - version output >>> (https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fd >>> r >>> i >>> ve.google.com%2Fopen%3Fid%3D1qu44Mk_aLz3d65YldDKo5mMtvJVyvb6D&da >>> t >>> a >>> =01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040 >>> f >>> 9 >>> %7C72654b74be024361a62716b132e3fdd0%7C0&sdata=UIVAn%2BTTdZx6ljvG >>> Q >>> l >>> %2FQA4jJM1A%2Bbz3dvK8YmGAoBd8%3D&reserved=0 ) >>> >>> Kind regards, >>> Chris. >>> >>> >>&g
Re: [gmx-users] EXTERNAL: Re: gromacs make check failure
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 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 > 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
Re: [gmx-users] EXTERNAL: Re: gromacs make check failure
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 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 > 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%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0&sdata=KY80wFoIdiVSSGMT%2BTzCwUATufKAFWEqKcmU%2Fm11zzQ%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%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0&sdata=3aLnTCJD%2FWtFronNOkYCl0jXr%2BQegYzYm%2BODizL7QdU%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%7C9a71d76a0c6d46f4a2e008d
[gmx-users] gromacs make check failure
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://drive.google.com/open?id=1tBs6scDqR_gJLtBRzpxMSEdbWwxYR5ks ) 2. Build output (https://drive.google.com/open?id=1PQFllv49M-Op6HLtdKsRJfwHbFeEsint ) 3. Dependency list (https://drive.google.com/open?id=13rETIX_ejMs1DPBGcTdsQfWKeYFNwd7T ) 4. Make checkout output (https://drive.google.com/open?id=1YpAEbPSj0eEe2JERbL6OIc49Gd5e57a1 ) 5. mdrun - version output (https://drive.google.com/open?id=1qu44Mk_aLz3d65YldDKo5mMtvJVyvb6D ) 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 -- 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.
[gmx-users] Gomacs 2019 build on sles12 and centos
Hi All, I've built Gromacs 2019 on both a CentOS 7 and SLES12 machine. Built using gcc@7.2.0 Dependencies: fftw@3.3.8 openmpi@3.1.3 When running "make check" on both machines, I'm getting the same timeout error for test 29 - see below for extract and attached for full test output anyone got any ideas? Thanks, Chris. === 29/40 Test #29: GmxPreprocessTests ...***Timeout 30.15 sec [==] Running 26 tests from 4 test cases. [--] Global test environment set-up. [--] 4 tests from GenconfTest [ RUN ] GenconfTest.nbox_Works [ OK ] GenconfTest.nbox_Works (186 ms) [ RUN ] GenconfTest.nbox_norenumber_Works [ OK ] GenconfTest.nbox_norenumber_Works (92 ms) [ RUN ] GenconfTest.nbox_dist_Works [ OK ] GenconfTest.nbox_dist_Works (372 ms) [ RUN ] GenconfTest.nbox_rot_Works center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 center of geometry: 1.733667, 1.477000, 0.905167 [ OK ] GenconfTest.nbox_rot_Works (471 ms) [--] 4 tests from GenconfTest (1121 ms total) [--] 5 tests from InsertMoleculesTest [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration Reading solute configuration Reading molecule configuration Initialising inter-atomic distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. 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 sprucea5:spack-build>make check [100%] Running all tests except physical validation /scratch/prod-spruce/acs/spack/opt/linux-sles12-x86_64/gcc-7.2.0/cmake-3.13.4-ocbi3jb2k4zbyt2lx7yvrm2ysb65nix6/bin/ctest --output-on-failure -E physicalvalidationtests Test project /ROWAN/group/pts/spack/dev-2019-02-19/var/spack/stage/gromacs-2019-55qcdjpc4twm5abmvt4kghka3eanxdc6/gromacs-2019/spack-build Start 1: TestUtilsUnitTests 1/40 Test #1: TestUtilsUnitTests ... Passed1.99 sec Start 2: TestUtilsMpiUnitTests 2/40 Test #2: TestUtilsMpiUnitTests Passed0.41 sec Start 3: MdlibUnitTest 3/40 Test #3: MdlibUnitTest Passed0.39 sec Start 4: AppliedForcesUnitTest 4/40 Test #4: AppliedForcesUnitTest Passed2.24 sec Start 5: ListedForcesTest 5/40 Test #5: ListedForcesTest . Passed1.29 sec Start 6: CommandLineUnitTests 6/40 Test #6: CommandLineUnitTests . Passed0.42 sec Start 7: DomDecTests 7/40 Test #7: DomDecTests .. Passed0.24 sec Start 8: EwaldUnitTests 8/40 Test #8: EwaldUnitTests ... Passed9.78 sec Start 9: FFTUnitTests 9/40 Test #9: FFTUnitTests . Passed0.48 sec Start 10: GpuUtilsUnitTests 10/40 Test #10: GpuUtilsUnitTests Passed0.23 sec Start 11: HardwareUnitTests 11/40 Test #11: HardwareUnitTests Passed0.24 sec Start 12: MathUnitTests 12/40 Test #12: MathUnitTests Passed4.02 sec Start 13: MdrunUtilityUnitTests 13/40 Test #13: MdrunUtilityUnitTests Passed0.25 sec Start 14: MdrunUtilityMpiUnitTests 14/40 Test #14: MdrunUtilityMpiUnitTests . Passed0.27 sec Start 15: OnlineHelpUnitTests 15/40 Test #15: OnlineHelpUnitTests .. Passed0.53 sec Start 16: OptionsUnitTests 16/40 Test #16: OptionsUnitTests . Passed2.04 sec Start 17: RandomUnitTests 17/40 Test #17: RandomUnitTests .. Passed0.50 sec Start 1
