[CP2K-user] [CP2K:11132] Re: van der Waals regtests fail on Intel KNL, and build glitches

Ronald Cohen reco... at gmail.com
Tue Jan 8 09:12:49 CET 2019


Thank you so much. I don’t have 18.03 installed. I was also having problem with earlier versions, but did not document so carefully
and did not run regtests. When I try my own job (not the regtest) with non-local vdW PSMP just never converges and it segfaults on the stress calculation.



Here is the end of the argon07 test:

 Leaving inner SCF loop after reaching     2 steps.


  Electronic density on regular grids:        -32.0000000000        0.0000000000
  Core density on regular grids:               31.9999999977       -0.0000000023
  Total charge density on r-space grids:       -0.0000000023
  Total charge density g-space grids:          -0.0000000023

  Overlap energy of the core charge distribution:               0.00000000000000
  Self energy of the core charge distribution:               -180.54066673528200
  Core Hamiltonian energy:                                     42.11893140752033
  Hartree energy:                                              68.47313966072379
  Exchange-correlation energy:                                -15.35702018709375
  Dispersion energy:                                            0.25474393253353

  Total energy:                                               -85.05087192159809

 *** WARNING in qs_scf.F:542 :: SCF run NOT converged ***

forrtl: severe (174): SIGSEGV, segmentation fault occurred
forrtl: severe (174): SIGSEGV, segmentation fault occurred
forrtl: severe (174): SIGSEGV, segmentation fault occurred
forrtl: severe (174): SIGSEGV, segmentation fault occurred
forrtl: severe (174): SIGSEGV, segmentation fault occurred
forrtl: severe (174): SIGSEGV, segmentation fault occurred
forrtl: severe (174): SIGSEGV, segmentation fault occurred
forrtl: severe (174): SIGSEGV, segmentation fault occurred
EXIT CODE:  174  MEANING:  RUNTIME FAIL
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---
Ron Cohen
reco... at gmail.com <mailto:reco... at gmail.com>
skypename: ronaldcohen
twitter: @recohen3




> On Jan 8, 2019, at 9:13 AM, Alfio Lazzaro <alfio.... at gmail.com> wrote:
> 
> Hi Ron,
> Could you share one of the FAILED logs? For instance the log of argon07.inp. The regtests script prints the last part of the log at the end of its execution... My suspicious is that these failing tests are dying because of a numerical assert in CP2K, so they can be included in the WRONG category. Now, you are saying that the problem comes from PSMP build, so my first try (very conservative) would be to use a single thread and see if it works. Note that CP2K tests with 2 threads (while you are using 4). Another possibility would be to avoid AVX512 vectorization (CP2K doesn't test it yet). Also, I have just realized that CP2K doesn't test 18.0.5 for PSMP and 19.x at all (see CP2K tests at https://dashboard.cp2k.org/ ). So, my suggestion is to reproduce what it is already tested by CP2K. A good starting point is this test
> 
> https://www.cp2k.org/static/regtest/trunk/swan-skl28/CRAY-XC40-intel-mkl.psmp_18.0.3.222.out
> 
> Alfio
> 
> 
> Il giorno lunedì 7 gennaio 2019 20:34:23 UTC+1, Ronald Cohen ha scritto:
> I did build also with precise but did not help. The values are very wrong , not slightly. Ron
> 
> Sent from my iPhone
> 
> On Jan 7, 2019, at 20:13, Anton Kudelin <arch... at gmail.com <javascript:>> wrote:
> 
>> Could you add "-fp-model precise" to CFLAGS and FCFLAGS? It won't fix 'RUNTIME FAIL', but could help with 'WRONG RESULT'.
>> 
>> On Monday, January 7, 2019 at 9:06:28 PM UTC+3, Ronald Cohen wrote:
>> So I tried:
>> 
>> export KMP_STACKSIZE=512M
>> rcohen at tomcat3:~/CP2K/cp2k$ ./tools/regtesting/do_regtest -arch Linux-x86-64-intel -version psmp -restrictdir QS/regtest-dft-vdw-corr-1/ -restrictdir QS/regtest-dft-vdw-corr-2/ -restrictdir QS/regtest-dft-vdw-corr-3/ -restrictdir QS/regtest-dft-vdw-corr-3/ -nobuild -mpiranks 4 -ompthreads 4 -maxtasks 16 |& tee testwith512MKMP_STACKSIZE.out &
>> and I still get:
>> 
>> < /home/rcohen/CP2K/cp2k/TEST-Linux-x86-64-intel-psmp-2019-01-07_18-24-16/tests/QS/regtest-dft-vdw-corr-3 (1 of 3) done in 775.00 sec
>> >>> /home/rcohen/CP2K/cp2k/TEST-Linux-x86-64-intel-psmp-2019-01-07_18-24-16/tests/QS/regtest-dft-vdw-corr-3
>>     argon05.inp                                               -85.02462435591488  WRONG RESULT TEST 1
>>     argon06.inp                                               -85.18989253445228  WRONG RESULT TEST 1
>>     argon07.inp                                               -85.05087192159809         RUNTIME FAIL
>>     argon08.inp                                               -85.05201740647929         RUNTIME FAIL
>>     argon09.inp                                               -85.05086520280044         RUNTIME FAIL
>>     argon10.inp                                               -85.05070440200512         RUNTIME FAIL
>>     argon11.inp                                               -84.69892988333885         RUNTIME FAIL
>>     argon12.inp                                               -84.69900817368848         RUNTIME FAIL
>>     argon13.inp                                               -84.81306482759408  WRONG RESULT TEST 1
>>     argon14.inp                                               -84.69889654472566  WRONG RESULT TEST 1
>>     argon-beef.inp                                            -42.46311172518392  WRONG RESULT TEST 1
>>     dftd3bj_t1.inp                                             -0.00355123783846     OK (   1.19 sec)
>>     dftd3bj_t2.inp                                             -0.05897356220363     OK (   2.20 sec)
>>     dftd3bj_t3.inp                                             -0.00112424003807     OK (   3.75 sec)
>>     dftd3bj_t4.inp                                                -84.2983390350     OK (   3.86 sec)
>> <<< /home/rcohen/CP2K/cp2k/TEST-Linux-x86-64-intel-psmp-2019-01-07_18-24-16/tests/QS/regtest-dft-vdw-corr-3 (1 of 3) done in 775.00 sec
>> Starting regression tests in /home/rcohen/CP2K/cp2k/TEST-Linux-x86-64-intel-psmp-2019-01-07_18-24-16/tests/QS/regtest-dft-vdw-corr-2 (2 of 3)
>> Starting regression tests in /home/rcohen/CP2K/cp2k/TEST-Linux-x86-64-intel-psmp-2019-01-07_18-24-16/tests/QS/regtest-dft-vdw-corr-2 (2 of 3)
>> 
>> 
>> Almost all of the non vdw routines pass.
>> 
>> Sincerely,
>> 
>> Ron
>> 
>> ---
>> Ron Cohen
>> rec... at gmail.com <>
>> skypename: ronaldcohen
>> twitter: @recohen3
>> 
>> 
>> 
>> 
>>> On Jan 7, 2019, at 6:12 PM, Robert Schade <robe... at uni-paderborn.de <>> wrote:
>>> 
>>> Signed PGP part
>>> Could you try setting KMP_STACKSIZE to something large in the terminal
>>> session with "export KMP_STACKSIZE=512m" before you rerun the regtests
>>> with your intel-psmp-binary that failed before?
>>> Please also make sure that the general stack size is not the problem
>>> by running "ulimt -s unlimited" in the same terminal where you want to
>>> execute the regtests.
>>> Best Wishes
>>> Robert
>>> 
>>> On 07.01.19 18:00, Ronald Cohen wrote:
>>> > BTW, in case it was not clear. My Intel builds of POPT and PSMP
>>> > versions were error free. The problems were all run time.
>>> >
>>> > Ron
>>> >
>>> > --- Ron Cohen rec... at gmail.com <> <mailto:... at gmail.com <>>
>>> > skypename: ronaldcohen twitter: @recohen3
>>> >
>>> >
>>> >
>>> >
>>> >> On Jan 7, 2019, at 5:39 PM, Robert Schade
>>> >> <robe... at uni-paderborn.de <>
>>> >> <mailto:rob... at uni-paderborn.de <>>> wrote:
>>> >>
>>> >> Signed PGP part r is automatically private because it is the
>>> >> first iteration variable. Every drho(s, i) is only read and
>>> >> written in exactly one loop iteration. The statement
>>> >> "COLLAPSE(3)" collapses the three perfectly nested loops into one
>>> >> loop. So, IMHO, this code looks ok. Best Wishes Robert
>>> >>
>>> >>
>>> >> On 07.01.19 14:52, Ronald Cohen wrote:
>>> >>> Yes, I agree. I have tried the 2018.05 and the 2019.1 intel
>>> >>> compilers. The POPT version runs fine, but the PSMP version
>>> >>> fails in the vDW routines. I find things like: in
>>> >>> qs_dispersion_nonloc.F
>>> >>>
>>> >>> !$OMP PARALLEL DO DEFAULT(NONE)                      & !$OMP
>>> >>> SHARED(ispin,i,n,lo,drho,drho_r)   & !$OMP
>>> >>> PRIVATE(s) & !$OMP             COLLAPSE(3) DO r = 0, n(3)-1 DO
>>> >>> q = 0, n(2)-1 DO p = 0, n(1)-1 s = r*n(2)*n(1)+q*n(1)+p+1
>>> >>> drho(s, i) = drho(s, i)+drho_r(i, ispin)%pw%cr3d(p+lo(1), q
>>> >>> +lo(2), r+lo(3)) END DO END DO END DO !$OMP END PARALLEL DO END
>>> >>> DO END DO
>>> >>>
>>> >>> Doesn’t this have to be marked as a reduction? And shouldn’t r,
>>> >>> q, p be labeled private? Perhaps this is automatic, but I do
>>> >>> not see that said anywhere. Does gnu treat such differently
>>> >>> than intel? Just ideas.
>>> >>>
>>> >>> I am currently trying the toolchain, but it is building
>>> >>> everything from scratch, including blas, lapack, scalapack etc
>>> >>> etc, so will take days.
>>> >>>
>>> >>> Thank you for your help,
>>> >>>
>>> >>> Sincerely,
>>> >>>
>>> >>> Ron
>>> >>>
>>> >>> --- Ron Cohen rec... at gmail.com <> <mailto:... at gmail.com <>>
>>> >> <mailto:... at gmail.com <>>
>>> >>> skypename: ronaldcohen twitter: @recohen3
>>> >>>
>>> >>>
>>> >>>
>>> >>>
>>> >>>> On Jan 7, 2019, at 2:16 PM, Robert Schade
>>> >>>> <robe... at uni-paderborn.de <>
>>> >>>> <mailto:rob... at uni-paderborn.de <>>
>>> >>>> <mailto:rob... at uni-paderborn.de <>>> wrote:
>>> >>>>
>>> >>>> Building cp2k on Intel Xeon Phi Knights Landing (KNL, not to
>>> >>>> be confused with KNC!) is not different from building it on
>>> >>>> any other Intel CPU. Hence, I think that the failing regtests
>>> >>>> point to an underlying issue. Which exact version of the
>>> >>>> Intel Compiler and MKL have you tried? Best Wishes Robert
>>> >>>>
>>> >>>> On 06.01.19 01:59, Ronald Cohen wrote:
>>> >>>>> OK—sorry for all the noise. I am trying:
>>> >>>>> ./install_cp2k_toolchain.sh --with-elpa=install
>>> >>>>> --with-libint=install --with-gcc=install I hate not being
>>> >>>>> able to use my intel tools which work for me for everything
>>> >>>>> else just fine.
>>> >>>>>
>>> >>>>> Ron
>>> >>>>>
>>> >>>>
>>> >>>> -- Robert Schade Paderborn Center for Parallel Computing
>>> >>>> (PC2) University of Paderborn Warburger Str. 100 D-33098
>>> >>>> Paderborn Germany robe... at uni-paderborn.de <>
>>> >> <mailto:rob... at uni-paderborn.de <>>
>>> >>>> <mailto:rob... at uni-paderborn.de <>> +49/(0)5251/60-5393
>>> >>>>
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>>> >>
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>>> >> -- Robert Schade Paderborn Center for Parallel Computing (PC2)
>>> >> University of Paderborn Warburger Str. 100 D-33098 Paderborn
>>> >> Germany robe... at uni-paderborn.de <>
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>>> --
>>> Robert Schade
>>> Paderborn Center for Parallel Computing (PC2)
>>> University of Paderborn
>>> Warburger Str. 100
>>> D-33098 Paderborn
>>> Germany
>>> robe... at uni-paderborn.de <>
>>> +49/(0)5251/60-5393
>>> 
>> 
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