Re: [gmx-users] Gomacs 2019 build on sles12 and centos
Hi, I assume the timeout does not happen with non-MPI builds, right? Have you tried a different MPI flavor? Cheers, -- Szilárd On Mon, Mar 11, 2019 at 10:54 AM Nelson Chris AWE wrote: > 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 > -- > 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. -- 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
