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susilehtola / erkale

ERKALE -- HF/DFT from Hel
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Some tests fail/hang on FreeBSD #29

Closed yurivict closed 5 years ago

yurivict commented 5 years ago

These tests fail:

        Start   5: H_dz_chk
  5/176 Test   #5: H_dz_chk .........................***Exception: Child aborted  0.51 sec
        Start   6: H_dz
  6/176 Test   #6: H_dz .............................***Exception: Child aborted  0.05 sec
        Start   7: He_dz_chk
  7/176 Test   #7: He_dz_chk ........................   Passed    0.19 sec
        Start   8: He_dz
  8/176 Test   #8: He_dz ............................   Passed    0.12 sec
        Start   9: H2_dz_chk
  9/176 Test   #9: H2_dz_chk ........................   Passed    0.12 sec
        Start  10: H2_dz
 10/176 Test  #10: H2_dz ............................***Exception: Child aborted  0.17 sec

Then, this test doesn't finish in 20 mins:

        Start  89: water_dimer_b97m_v_chk

FreeBSD 11.2 amd64

susilehtola commented 5 years ago

This is the same issue as #18.

I'm not sure test 89 running 20 mins makes sense. Which architecture? Which processor? If you're running with a single core and a slow processor it's very well possible the calculation takes a long time since the VV10 kernel takes a long time.

yurivict commented 5 years ago

Indeed, nothing freezes, only 17 failures:

90% tests passed, 17 tests failed out of 176

Total Test time (real) = 7707.66 sec

The following tests FAILED:
      5 - H_dz_chk (Child aborted)
      6 - H_dz (Child aborted)
     10 - H2_dz (Child aborted)
     99 - water_dimer_rihf_chk (Child aborted)
    100 - water_dimer_rihf (Child aborted)
    110 - water_dimer_b3lyp_fch (Child aborted)
    114 - water_dimer_b3lyp_xrs (Child aborted)
    126 - water_dimer_pbe0_xrs (Child aborted)
    128 - water_dimer_pbe_fch (Child aborted)
    134 - water_dimer_tpssh_fch (Child aborted)
    136 - water_dimer_tpssh_xch (Child aborted)
    138 - water_dimer_tpssh_xrs (Child aborted)
    144 - water_dimer_wb97x_fch (Child aborted)
    167 - water_cluster_fch_chk (Child aborted)
    168 - water_cluster_fch (Child aborted)
    175 - decanol_chk (Child aborted)
    176 - decanol (Child aborted)
Errors while running CTest
*** Error code 8
yurivict commented 5 years ago

A lot more tests fail with the parallel version:

        Start   1: build_basictests
  1/176 Test   #1: build_basictests .................   Passed    1.91 sec
        Start   2: basictests
  2/176 Test   #2: basictests .......................***Exception: SegFault  1.57 sec
        Start   3: build_erkale
  3/176 Test   #3: build_erkale .....................   Passed    1.60 sec
        Start   4: build_chkcompare
  4/176 Test   #4: build_chkcompare .................   Passed    2.43 sec
        Start   5: H_dz_chk
  5/176 Test   #5: H_dz_chk .........................***Exception: Child aborted  0.77 sec
        Start   6: H_dz
  6/176 Test   #6: H_dz .............................***Exception: Child aborted  0.22 sec
        Start   7: He_dz_chk
  7/176 Test   #7: He_dz_chk ........................   Passed    0.32 sec
        Start   8: He_dz
  8/176 Test   #8: He_dz ............................   Passed    0.26 sec
        Start   9: H2_dz_chk
  9/176 Test   #9: H2_dz_chk ........................   Passed    0.29 sec
        Start  10: H2_dz
 10/176 Test  #10: H2_dz ............................***Exception: Child aborted  0.66 sec
        Start  11: H2_lda_dz_chk
 11/176 Test  #11: H2_lda_dz_chk ....................***Exception: SegFault  0.58 sec
        Start  12: H2_lda_dz
 12/176 Test  #12: H2_lda_dz ........................***Exception: Child aborted  0.36 sec
        Start  13: H2_pbe_dz_chk
 13/176 Test  #13: H2_pbe_dz_chk ....................***Exception: SegFault  0.60 sec
        Start  14: H2_pbe_dz
 14/176 Test  #14: H2_pbe_dz ........................***Exception: Child aborted  0.54 sec
        Start  15: Be_dz_chk
 15/176 Test  #15: Be_dz_chk ........................   Passed    0.98 sec
        Start  16: Be_dz
 16/176 Test  #16: Be_dz ............................   Passed    4.27 sec
        Start  17: Be+_dz_chk
 17/176 Test  #17: Be+_dz_chk .......................***Exception: SegFault  6.33 sec
        Start  18: Be+_dz
 18/176 Test  #18: Be+_dz ...........................   Passed    1.61 sec
        Start  19: Ne_dz_chk
 19/176 Test  #19: Ne_dz_chk ........................***Exception: SegFault  2.23 sec
        Start  20: Ne_dz
 20/176 Test  #20: Ne_dz ............................***Exception: Child aborted  0.27 sec
        Start  21: Ne_dz_cart_chk
 21/176 Test  #21: Ne_dz_cart_chk ...................***Exception: SegFault  0.83 sec
        Start  22: Ne_dz_cart
 22/176 Test  #22: Ne_dz_cart .......................***Exception: Child aborted  0.18 sec
        Start  23: Mg_dz_chk
 23/176 Test  #23: Mg_dz_chk ........................***Exception: SegFault  2.08 sec
        Start  24: Mg_dz
 24/176 Test  #24: Mg_dz ............................***Exception: Child aborted  0.17 sec
        Start  25: Mg+_dz_chk
 25/176 Test  #25: Mg+_dz_chk .......................***Exception: SegFault  0.47 sec
        Start  26: Mg+_dz
 26/176 Test  #26: Mg+_dz ...........................***Exception: Child aborted  0.04 sec
        Start  27: Ne_lda_tz_chk
 27/176 Test  #27: Ne_lda_tz_chk ....................***Exception: SegFault  0.29 sec
        Start  28: Ne_lda_tz
 28/176 Test  #28: Ne_lda_tz ........................***Exception: Child aborted  0.04 sec
        Start  29: Ne_pbe_tz_chk
 29/176 Test  #29: Ne_pbe_tz_chk ....................***Exception: SegFault  0.32 sec
        Start  30: Ne_pbe_tz
 30/176 Test  #30: Ne_pbe_tz ........................***Exception: Child aborted  0.11 sec
        Start  31: Ne_tpss_tz_chk
 31/176 Test  #31: Ne_tpss_tz_chk ...................***Exception: SegFault  0.38 sec
        Start  32: Ne_tpss_tz
 32/176 Test  #32: Ne_tpss_tz .......................***Exception: Child aborted  0.02 sec
        Start  33: Ne_tz_chk
 33/176 Test  #33: Ne_tz_chk ........................***Exception: SegFault  0.36 sec
        Start  34: Ne_tz
 34/176 Test  #34: Ne_tz ............................***Exception: Child aborted  0.08 sec
        Start  35: Mg_lda_tz_chk
 35/176 Test  #35: Mg_lda_tz_chk ....................***Exception: SegFault  0.31 sec
        Start  36: Mg_lda_tz
 36/176 Test  #36: Mg_lda_tz ........................***Exception: Child aborted  0.03 sec
        Start  37: Mg+_lda_tz_chk
 37/176 Test  #37: Mg+_lda_tz_chk ...................***Exception: SegFault  0.27 sec
        Start  38: Mg+_lda_tz
 38/176 Test  #38: Mg+_lda_tz .......................***Exception: Child aborted  0.02 sec
        Start  39: Mg_pbe_tz_chk
 39/176 Test  #39: Mg_pbe_tz_chk ....................***Exception: SegFault  0.23 sec
        Start  40: Mg_pbe_tz
 40/176 Test  #40: Mg_pbe_tz ........................***Exception: Child aborted  0.04 sec
        Start  41: Mg+_pbe_tz_chk
 41/176 Test  #41: Mg+_pbe_tz_chk ...................***Exception: SegFault  0.22 sec
        Start  42: Mg+_pbe_tz
 42/176 Test  #42: Mg+_pbe_tz .......................***Exception: Child aborted  0.02 sec
        Start  43: Mg+_rohf_tz_chk
 43/176 Test  #43: Mg+_rohf_tz_chk ..................***Exception: SegFault  0.41 sec
        Start  44: Mg+_rohf_tz
 44/176 Test  #44: Mg+_rohf_tz ......................***Exception: Child aborted  0.05 sec
        Start  45: Mg_tpss_tz_chk
 45/176 Test  #45: Mg_tpss_tz_chk ...................***Exception: SegFault  0.21 sec
        Start  46: Mg_tpss_tz
 46/176 Test  #46: Mg_tpss_tz .......................***Exception: Child aborted  0.11 sec
        Start  47: Mg+_tpss_tz_chk
^C*** Signal 2
yurivict commented 5 years ago

Do all these test failures prevent erkale's normal use?

susilehtola commented 5 years ago

What is the segfault caused by? You should find the core dumps under the tests/ directory of your object directory. The problems with the sequential version probably aren't a cause for worry; that might be just a compiler bug; but nothing should be segfaulting...

yurivict commented 5 years ago

It's a recurring (cyclic) exception:

(gdb) r /usr/ports/science/erkale/work-sequential/erkale-3608602/tests/water_dimer_rihf.run
The program being debugged has been started already.
Start it from the beginning? (y or n) y
Starting program: /usr/local/bin/erkale /usr/ports/science/erkale/work-sequential/erkale-3608602/tests/water_dimer_rihf.run
ERKALE - HF/DFT from Hel, serial version.
(c) Susi Lehtola, 2010-2016.

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

Running on host xxx.xxx.xxx.

Current time is Sat 17 Nov 2018 01:27:54.

Current Settings used by ERKALE:
     AtomGuess                          Auto    Method used for atomic guess (Auto for same as method)
     Basis                       aug-cc-pVDZ    Basis set used in calculation
     BasisCutoff                   1.000e-08    Cutoff for dropping out small primitives from contraction
     BasisOrth                          Auto    Method of orthonormalization of basis set
     BasisRotate                       false    Rotate basis set to remove redundant functions?
     Charge                                0    Total charge of system
     Cholesky                           true    Use Cholesky decomposition?
     CholeskyMode                          0    Save/load integrals? 0 no, 1 save, -1 load
     CholeskyNAFThr                0.000e+00    Cholesky natural auxiliary function threshold
     CholeskyShThr                 1.000e-02    Cholesky cache threshold
     CholeskyThr                   1.000e-07    Cholesky decomposition threshold
     ConvThr                       1.000e-06    Orbital gradient convergence threshold
     DIISComb                          false    Combine alpha and beta errors in unrestricted calcs?
     DIISEps                       1.000e-01    Start mixing in DIIS when error is
     DIISOrder                            10    How many DIIS iterations to keep in memory?
     DIISThr                       1.000e-02    DIIS error threshold for DIIS updates
     DecFock                           false    Use decontracted basis to calculate Fock matrix (direct HF)
     Decontract                                 Indices of atoms to decontract basis set for
     DensityFitting                     true    Use density fitting / RI?
     DimerSymmetry                     false    Do special calculation on dimer along z axis
     Direct                            false    Calculate two-electron integrals (or density fitting) on-the-fly?
     EField                      0.0 0.0 0.0    Electric field
     FittingBasis             aug-cc-pVDZ-JK    Basis to use for density fitting / RI (Auto for automatic)
     FittingMemory                      1000    Amount of memory in MB to use for exchange fitting
     FittingThreshold              1.000e-08    Linear dependence threshold for Coulomb integrals in density fitting
     ForcePol                          false    Force polarized calculation
     Guess                            Atomic    Used guess: SAD (default), NO, core, or GWH
     InputBohr                         false    Use atomic units as input units instead of angstrom?
     IntegralThresh                1.000e-14    Integral screening threshold
     LoadChk                                    File to load old results from
     Logfile            water_dimer_rihf.log    File to print out full information, stdout for screen
     MaxIter                             100    Maximum number of iterations in SCF cycle
     Method                               HF    Method used in calculation (HF or a DFT functional)
     Multiplicity                          1    Spin multiplicity
     Occupancies                                Orbital occupancies
     OptLM                              true    If spherical harmonics used, use cartesian s and p functions?
     SaveChk            water_dimer_rihf.chk    File to use as checkpoint
     Shift                         0.000e+00    Level shift to use in Hartree
     StrictIntegrals                   false    Use strict integrals?
     System                  water_dimer.xyz    System as an xyz file
     TRRHminS                      9.750e-01    Trust-Region Roothaan-Hall minimal occupied orbital overlap
     UseADIIS                           true    Use ADIIS for Fock matrix interpolation?
     UseBroyden                        false    Use Broyden mixing of Fock matrices?
     UseDIIS                            true    Use Pulay's Direct Inversion in the Iterative Subspace?
     UseLM                              true    Use a spherical harmonics basis set by default?
     UseTRRH                           false    Use Trust-Region Roothaan-Hall?
     Verbose                            true    Verbose calculation?

Breakpoint 1, __cxa_throw (thrown_exception=0x806439660, tinfo=0x607570 <typeinfo for std::runtime_error>, dest=0x401d40 <std::runtime_error::~runtime_error()@plt>)
    at /usr/src/contrib/libcxxrt/exception.cc:793
793     ex->referenceCount = 1;
(gdb) c
Continuing.

Breakpoint 6, __cxa_begin_catch (e=0x806439640) at /usr/src/contrib/libcxxrt/exception.cc:1222
1222    {
(gdb) c
Continuing.

Breakpoint 1, __cxa_throw (thrown_exception=0x806439520, tinfo=0x607570 <typeinfo for std::runtime_error>, dest=0x401d40 <std::runtime_error::~runtime_error()@plt>)
    at /usr/src/contrib/libcxxrt/exception.cc:793
793     ex->referenceCount = 1;
(gdb) c
Continuing.

Breakpoint 6, __cxa_begin_catch (e=0x806439500) at /usr/src/contrib/libcxxrt/exception.cc:1222
1222    {
(gdb) c
Continuing.

Breakpoint 1, __cxa_throw (thrown_exception=0x806439660, tinfo=0x607570 <typeinfo for std::runtime_error>, dest=0x401d40 <std::runtime_error::~runtime_error()@plt>)
    at /usr/src/contrib/libcxxrt/exception.cc:793
793     ex->referenceCount = 1;
(gdb) c
Continuing.

Breakpoint 6, __cxa_begin_catch (e=0x806439640) at /usr/src/contrib/libcxxrt/exception.cc:1222
1222    {
(gdb) c
Continuing.

Breakpoint 1, __cxa_throw (thrown_exception=0x8064381c0, tinfo=0x607570 <typeinfo for std::runtime_error>, dest=0x401d40 <std::runtime_error::~runtime_error()@plt>)
    at /usr/src/contrib/libcxxrt/exception.cc:793
793     ex->referenceCount = 1;
(gdb) c
Continuing.

Breakpoint 6, __cxa_begin_catch (e=0x8064381a0) at /usr/src/contrib/libcxxrt/exception.cc:1222
1222    {
(gdb) c
Continuing.

Breakpoint 1, __cxa_throw (thrown_exception=0x806438300, tinfo=0x607570 <typeinfo for std::runtime_error>, dest=0x401d40 <std::runtime_error::~runtime_error()@plt>)
    at /usr/src/contrib/libcxxrt/exception.cc:793
793     ex->referenceCount = 1;
(gdb)
susilehtola commented 5 years ago

Compile the code with proper debug flags please, this is not saying where the problem arises.

It might be a problem in libcxxrt; the code works just fine with glibc.

yurivict commented 5 years ago

For the testcase water_dimer_rihf.run it throws the exception Could not find basis for element O with atom number 1 in library! at src/basislibrary.cpp:2176.

This never gets actually printed.

Then it throws another exception: Could not find basis for element H with atom number 2 in library!

This also is never printed.

Same with Could not find basis for element H with atom number 3 in library! And Could not find basis for element O with atom number 4 in library!

So on and so forth.

When I add my own printing line (printf or std::cout<<), these are also never printed for some reason.

Eventually src/scf-base.cpp:139 throws the exception ("Can't enable both Cholesky and density fitting!\n") that isn't caught and this causes SIGABORT.

susilehtola commented 5 years ago

Right, since instead of running the test suite you're now running the program separately without having passed the necessary environment variables - it doesn't know where the basis sets reside. Set ERKALE_LIBRARY properly and try again.

yurivict commented 5 years ago

Oh no, I do supply these variables:

cd /usr/ports/science/erkale/work-sequential/erkale-3608602/tests && \
ERKALE_SYSDIR=xyz ERKALE_LIBRARY=../basis/ ../../.build/src/erkale \
/usr/ports/science/erkale/work-sequential/erkale-3608602/tests/water_dimer_rihf.run

Only water_dimer_rihf.run fails, others, like Ne_qz.run don't fail.

susilehtola commented 5 years ago

OK, I realize there were conflicting options in a few tests since I had changed the defaults at some point; this is fixed in #32.

yurivict commented 5 years ago

At least H2_dz still fails.

susilehtola commented 5 years ago

And that's a weird failure - it fails in the test of the electron momentum density transform, which works for everything else, however. There's a tiny numerical difference in <p^2>/2 vs T for H2; this has worked before perfectly. It shouldn't be a huge problem though.

susilehtola commented 5 years ago

What's the thing with your segfaults?

yurivict commented 5 years ago

Revision 9f5593b has 10 failing tests (down from 17 before):

The following tests FAILED:
     10 - H2_dz (Child aborted)
    100 - water_dimer_rihf (Child aborted)
    110 - water_dimer_b3lyp_fch (Child aborted)
    114 - water_dimer_b3lyp_xrs (Child aborted)
    126 - water_dimer_pbe0_xrs (Child aborted)
    128 - water_dimer_pbe_fch (Child aborted)
    134 - water_dimer_tpssh_fch (Child aborted)
    136 - water_dimer_tpssh_xch (Child aborted)
    138 - water_dimer_tpssh_xrs (Child aborted)
    144 - water_dimer_wb97x_fch (Child aborted)

water_dimer_wb97x_fch and water_dimer_tpssh_xrs fail with exception:

Cannot recognize keyword XRSMethod!

The problem also is that erkale doesn't process exceptions properly, so it is necessary to build with debug info and use debugger, that makes troubleshooting more difficult.

susilehtola commented 5 years ago

"The problem also is that erkale doesn't process exceptions properly,"

Uhh.. what do you mean by this?

Exceptions crash the program when they are meant to do so.

Debugging always requires to build with debuginfo. All distributions build with it, and package it separately, so meaningful backtraces can be reported when a package is not working for some reason or another.

This still does not explain your original problem report where all the tests segfaulted.

susilehtola commented 5 years ago

All tests should work now, please confirm.

yurivict commented 5 years ago

water_dimer_wb97x_fch.run still fails:

Current time is Thu 22 Nov 2018 00:07:37.

Error in function parse (file /usr/ports/science/erkale/work-sequential/erkale-0927d8c/src/settings.cpp, near line 498)

Current Settings used by ERKALE:
     AtomGuess                          Auto    Method used for atomic guess (Auto for same as method)
     Basis                       aug-cc-pVDZ    Basis set used in calculation
     BasisCutoff                   1.000e-08    Cutoff for dropping out small primitives from contraction
     BasisOrth                          Auto    Method of orthonormalization of basis set
     BasisRotate                        true    Rotate basis set to remove redundant functions?
     Charge                                0    Total charge of system
     Cholesky                           true    Use Cholesky decomposition?
     CholeskyMode                          0    Save/load integrals? 0 no, 1 save, -1 load
     CholeskyNAFThr                0.000e+00    Cholesky natural auxiliary function threshold
     CholeskyShThr                 1.000e-02    Cholesky cache threshold
     CholeskyThr                   1.000e-07    Cholesky decomposition threshold
     ConvThr                       1.000e-06    Orbital gradient convergence threshold
     DFTDelta                      1.000e+02    Switch to final DFT grid has converged within factor X
     DFTFinalTol                   1.000e-05    Tolerance of final DFT grid
     DFTGrid                         50 -194    DFT integration grid to use: nrad lmax or Auto for adaptive
     DFTInitialTol                 1.000e-04    Tolerance of initial DFT grid
     DFTLobatto                        false    Use Lobatto quadrature instead of Lebedev quadrature?
     DIISComb                          false    Combine alpha and beta errors in unrestricted calcs?
     DIISEps                       1.000e-01    Start mixing in DIIS when error is
     DIISOrder                            10    How many DIIS iterations to keep in memory?
     DIISThr                       1.000e-02    DIIS error threshold for DIIS updates
     DecFock                           false    Use decontracted basis to calculate Fock matrix (direct HF)
     Decontract                                 Indices of atoms to decontract basis set for
     DensityFitting                    false    Use density fitting / RI?
     DimerSymmetry                     false    Do special calculation on dimer along z axis
     Direct                            false    Calculate two-electron integrals (or density fitting) on-the-fly?
     EField                      0.0 0.0 0.0    Electric field
     FittingBasis                       Auto    Basis to use for density fitting / RI (Auto for automatic)
     FittingMemory                      1000    Amount of memory in MB to use for exchange fitting
     FittingThreshold              1.000e-08    Linear dependence threshold for Coulomb integrals in density fitting
     ForcePol                          false    Force polarized calculation
     Guess                            Atomic    Used guess: SAD (default), NO, core, or GWH
     InputBohr                         false    Use atomic units as input units instead of angstrom?
     IntegralThresh                1.000e-14    Integral screening threshold
     LoadChk                                    File to load old results from
     Logfile                      erkale.log    File to print out full information, stdout for screen
     MaxIter                             100    Maximum number of iterations in SCF cycle
     Method                 hyb_gga_xc_wb97x    Method used in calculation (HF or a DFT functional)
     Multiplicity                          1    Spin multiplicity
     NLGrid                          50 -194    Integration grid to use for nonlocal correlation: nrad lmax
     Occupancies                                Orbital occupancies
     OptLM                              true    If spherical harmonics used, use cartesian s and p functions?
     PZ                                false    Perform Perdew-Zunger self-interaction correction?
     PZEthr                        1.000e-10    Threshold for energy convergence
     PZIthr                        1.000e-02    Threshold for initialization convergence (not too small!)
     PZNRthr                       0.000e+00    Threshold for use of NR method in OO optimization
     PZOOthr                       1.000e-04    Gradient threshold for OO optimization
     PZOVthr                       1.000e-05    Gradient threshold for OV optimization
     PZimag                             Auto    Imaginary degrees of freedom in PZ?
     PZiter                               20    Max number of iterations in self-consistency iteration
     PZloc                              Auto    Initial localization before SIC calculation?
     PZlocmet                             FB    Initial localization method (recommend FB or IAO)
     PZmode                               XC    Apply PZ to the operators (in addition to J): X C D
     PZoo                               true    Optimize OO block?
     PZov                               true    Optimize OV block?
     PZprec                                1    Precondition OV block? 0: no, 1: unified, 2: orbital
     PZscale                        Constant    Scaling for PZ: Constant, Density or Kinetic
     PZscaleExp                    1.000e+00    Exponent in the dynamic scaling equation
     PZseed                                0    Seed number for randomized matrices?
     PZstab                                0    Stability analysis for PZ-SIC? 1 or -1 for OO, 2 or -2 for OO+OV
     PZstabThr                     1.000e-03    Instability threshold (interpreted as -thr)
     PZw                           1.000e+00    Weight for Perdew-Zunger self-interaction correction
     SaveChk                      erkale.chk    File to use as checkpoint
     Shift                         0.000e+00    Level shift to use in Hartree
     StrictIntegrals                   false    Use strict integrals?
     System              water_dimer_xrs.xyz    System as an xyz file
     TRRHminS                      9.750e-01    Trust-Region Roothaan-Hall minimal occupied orbital overlap
     UseADIIS                           true    Use ADIIS for Fock matrix interpolation?
     UseBroyden                        false    Use Broyden mixing of Fock matrices?
     UseDIIS                            true    Use Pulay's Direct Inversion in the Iterative Subspace?
     UseLM                              true    Use a spherical harmonics basis set by default?
     UseTRRH                           false    Use Trust-Region Roothaan-Hall?
     VV10                               Auto    Use VV10 non-local correlation?
     VV10Pars                                   VV10 parameters: b C
     Verbose                            true    Verbose calculation?

Abort trap

To compare, Ne_lda_tz.run succeeds. I run with this line:

ERKALE_SYSDIR=tests/xyz ERKALE_LIBRARY=basis/ ../.build/src/erkale tests/$TEST
susilehtola commented 5 years ago

Please run ctest.

yurivict commented 5 years ago

---sequential failures---

UpdateCTestConfiguration  from :/usr/ports/science/erkale/work-sequential/.build/DartConfiguration.tcl
UpdateCTestConfiguration  from :/usr/ports/science/erkale/work-sequential/.build/DartConfiguration.tcl
Test project /usr/ports/science/erkale/work-sequential/.build
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 135
    Start 135: water_dimer_tpssh_xch_chk

135: Test command: /usr/ports/science/erkale/work-sequential/.build/src/xrs/erkale_xrs "/usr/ports/science/erkale/work-sequential/erkale-0927d8c/tests/water_dimer_tpssh_xch.run"
135: Environment variables: 
135:  ERKALE_SYSDIR=/usr/ports/science/erkale/work-sequential/erkale-0927d8c/tests/xyz
135:  ERKALE_LIBRARY=/usr/ports/science/erkale/work-sequential/erkale-0927d8c/basis
135: Test timeout computed to be: 10000000
135: ERKALE - XRS from Hel, serial version.
135: (c) Susi Lehtola, 2010-2016.
135: 
135: This program is free software; you can redistribute it and/or modify
135: it under the terms of the GNU General Public License as published by
135: the Free Software Foundation; either version 2 of the License, or
135: (at your option) any later version.
135: 
135: Running on host yv.noip.me.
135: 
135: Current time is Thu 22 Nov 2018 09:15:53.
135: 
135: HDF5-DIAG: Error detected in HDF5 (1.10.2) thread 0:
135:   #000: H5F.c line 511 in H5Fopen(): unable to open file
135:     major: File accessibilty
135:     minor: Unable to open file
135:   #001: H5Fint.c line 1604 in H5F_open(): unable to read superblock
135:     major: File accessibilty
135:     minor: Read failed
135:   #002: H5Fsuper.c line 630 in H5F__super_read(): truncated file: eof = 638906, sblock->base_addr = 0, stored_eof = 747562
135:     major: File accessibilty
135:     minor: File has been truncated
135: HDF5-DIAG: Error detected in HDF5 (1.10.2) thread 0:
135:   #000: H5L.c line 819 in H5Lexists(): not a location
135:     major: Invalid arguments to routine
135:     minor: Inappropriate type
135:   #001: H5Gloc.c line 251 in H5G_loc(): invalid object ID
135:     major: Invalid arguments to routine
135:     minor: Bad value
135: HDF5-DIAG: Error detected in HDF5 (1.10.2) thread 0:
135:   #000: H5L.c line 819 in H5Lexists(): not a location
135:     major: Invalid arguments to routine
135:     minor: Inappropriate type
135:   #001: H5Gloc.c line 251 in H5G_loc(): invalid object ID
135:     major: Invalid arguments to routine
135:     minor: Bad value
135: HDF5-DIAG: Error detected in HDF5 (1.10.2) thread 0:
135:   #000: H5D.c line 284 in H5Dopen2(): not a location
135:     major: Invalid arguments to routine
135:     minor: Inappropriate type
135:   #001: H5Gloc.c line 251 in H5G_loc(): invalid object ID
135:     major: Invalid arguments to routine
135:     minor: Bad value
135: HDF5-DIAG: Error detected in HDF5 (1.10.2) thread 0:
135:   #000: H5D.c line 447 in H5Dget_type(): not a dataset
135:     major: Invalid arguments to routine
135:     minor: Inappropriate type
135: HDF5-DIAG: Error detected in HDF5 (1.10.2) thread 0:
135:   #000: H5D.c line 373 in H5Dget_space(): not a dataset
135:     major: Invalid arguments to routine
135:     minor: Inappropriate type
135: HDF5-DIAG: Error detected in HDF5 (1.10.2) thread 0:
135:   #000: H5T.c line 1856 in H5Tget_class(): not a datatype
135:     major: Invalid arguments to routine
135:     minor: Inappropriate type
1/2 Test #135: water_dimer_tpssh_xch_chk ........***Exception: Child aborted  0.03 sec
test 136
    Start 136: water_dimer_tpssh_xch

136: Test command: /usr/ports/science/erkale/work-sequential/.build/src/test/chkcompare "water_dimer_tpssh_xch.chk"
136: Environment variables: 
136:  ERKALE_REFDIR=/usr/ports/science/erkale/work-sequential/erkale-0927d8c/refdata
136: Test timeout computed to be: 10000000
136: Reference directory is set to "/usr/ports/science/erkale/work-sequential/erkale-0927d8c/refdata".
136: HDF5-DIAG: Error detected in HDF5 (1.10.2) thread 0:
136:   #000: H5F.c line 511 in H5Fopen(): unable to open file
136:     major: File accessibilty
136:     minor: Unable to open file
136:   #001: H5Fint.c line 1604 in H5F_open(): unable to read superblock
136:     major: File accessibilty
136:     minor: Read failed
136:   #002: H5Fsuper.c line 630 in H5F__super_read(): truncated file: eof = 638906, sblock->base_addr = 0, stored_eof = 747562
136:     major: File accessibilty
136:     minor: File has been truncated
136: HDF5-DIAG: Error detected in HDF5 (1.10.2) thread 0:
136:   #000: H5L.c line 819 in H5Lexists(): not a location
136:     major: Invalid arguments to routine
136:     minor: Inappropriate type
136:   #001: H5Gloc.c line 251 in H5G_loc(): invalid object ID
136:     major: Invalid arguments to routine
136:     minor: Bad value
136: HDF5-DIAG: Error detected in HDF5 (1.10.2) thread 0:
136:   #000: H5L.c line 819 in H5Lexists(): not a location
136:     major: Invalid arguments to routine
136:     minor: Inappropriate type
136:   #001: H5Gloc.c line 251 in H5G_loc(): invalid object ID
136:     major: Invalid arguments to routine
136:     minor: Bad value
136: HDF5-DIAG: Error detected in HDF5 (1.10.2) thread 0:
136:   #000: H5D.c line 284 in H5Dopen2(): not a location
136:     major: Invalid arguments to routine
136:     minor: Inappropriate type
136:   #001: H5Gloc.c line 251 in H5G_loc(): invalid object ID
136:     major: Invalid arguments to routine
136:     minor: Bad value
136: HDF5-DIAG: Error detected in HDF5 (1.10.2) thread 0:
136:   #000: H5D.c line 447 in H5Dget_type(): not a dataset
136:     major: Invalid arguments to routine
136:     minor: Inappropriate type
136: HDF5-DIAG: Error detected in HDF5 (1.10.2) thread 0:
136:   #000: H5D.c line 373 in H5Dget_space(): not a dataset
136:     major: Invalid arguments to routine
136:     minor: Inappropriate type
136: HDF5-DIAG: Error detected in HDF5 (1.10.2) thread 0:
136:   #000: H5T.c line 1856 in H5Tget_class(): not a datatype
136:     major: Invalid arguments to routine
136:     minor: Inappropriate type
2/2 Test #136: water_dimer_tpssh_xch ............***Exception: Child aborted  0.01 sec

0% tests passed, 2 tests failed out of 2

Total Test time (real) =   0.05 sec

The following tests FAILED:
    135 - water_dimer_tpssh_xch_chk (Child aborted)
    136 - water_dimer_tpssh_xch (Child aborted)

---parallel failures---

$ ctest -V -R water_dimer_wb97x_fch
UpdateCTestConfiguration  from :/usr/ports/science/erkale/work-parallel/.build/DartConfiguration.tcl
UpdateCTestConfiguration  from :/usr/ports/science/erkale/work-parallel/.build/DartConfiguration.tcl
Test project /usr/ports/science/erkale/work-parallel/.build
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 143
    Start 143: water_dimer_wb97x_fch_chk

143: Test command: /usr/ports/science/erkale/work-parallel/.build/src/xrs/erkale_xrs_omp "/usr/ports/science/erkale/work-parallel/erkale-0927d8c/tests/water_dimer_wb97x_fch.run"
143: Environment variables: 
143:  ERKALE_SYSDIR=/usr/ports/science/erkale/work-parallel/erkale-0927d8c/tests/xyz
143:  ERKALE_LIBRARY=/usr/ports/science/erkale/work-parallel/erkale-0927d8c/basis
143: Test timeout computed to be: 10000000
143: ERKALE - XRS from Hel, OpenMP version, running on 8 cores.
143: (c) Susi Lehtola, 2010-2016.
143: 
143: This program is free software; you can redistribute it and/or modify
143: it under the terms of the GNU General Public License as published by
143: the Free Software Foundation; either version 2 of the License, or
143: (at your option) any later version.
143: 
143: Running on host xxx.noip.me.
143: 
143: Current time is Thu 22 Nov 2018 07:09:56.
143: 
143: No converged calculation found in SaveChk.
1/2 Test #143: water_dimer_wb97x_fch_chk ........***Exception: Child aborted  0.07 sec
test 144
    Start 144: water_dimer_wb97x_fch

144: Test command: /usr/ports/science/erkale/work-parallel/.build/src/test/chkcompare_omp "water_dimer_wb97x_fch.chk"
144: Environment variables: 
144:  ERKALE_REFDIR=/usr/ports/science/erkale/work-parallel/erkale-0927d8c/refdata
144: Test timeout computed to be: 10000000
144: Reference directory is set to "/usr/ports/science/erkale/work-parallel/erkale-0927d8c/refdata".
2/2 Test #144: water_dimer_wb97x_fch ............***Exception: Child aborted  0.01 sec

0% tests passed, 2 tests failed out of 2

Total Test time (real) =   0.09 sec

The following tests FAILED:
    143 - water_dimer_wb97x_fch_chk (Child aborted)
    144 - water_dimer_wb97x_fch (Child aborted)
Errors while running CTest
UpdateCTestConfiguration  from :/usr/ports/science/erkale/work-parallel/.build/DartConfiguration.tcl
UpdateCTestConfiguration  from :/usr/ports/science/erkale/work-parallel/.build/DartConfiguration.tcl
Test project /usr/ports/science/erkale/work-parallel/.build
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 19
    Start 19: Ne_dz_chk

19: Test command: /usr/ports/science/erkale/work-parallel/.build/src/erkale_omp "/usr/ports/science/erkale/work-parallel/erkale-0927d8c/tests/Ne_dz.run"
19: Environment variables: 
19:  ERKALE_SYSDIR=/usr/ports/science/erkale/work-parallel/erkale-0927d8c/tests/xyz
19:  ERKALE_LIBRARY=/usr/ports/science/erkale/work-parallel/erkale-0927d8c/basis
19: Test timeout computed to be: 10000000
19: ERKALE - HF/DFT from Hel, OpenMP version, running on 8 cores.
19: (c) Susi Lehtola, 2010-2016.
19: 
19: This program is free software; you can redistribute it and/or modify
19: it under the terms of the GNU General Public License as published by
19: the Free Software Foundation; either version 2 of the License, or
19: (at your option) any later version.
19: 
19: Running on host yv.noip.me.
19: 
19: Current time is Thu 22 Nov 2018 09:17:24.
19: 
19: Current Settings used by ERKALE:
19:      AtomGuess                          Auto    Method used for atomic guess (Auto for same as method)
19:      Basis                           cc-pVDZ    Basis set used in calculation
19:      BasisCutoff                   1.000e-08    Cutoff for dropping out small primitives from contraction
19:      BasisOrth                          Auto    Method of orthonormalization of basis set
19:      BasisRotate                       false    Rotate basis set to remove redundant functions?
19:      Charge                                0    Total charge of system
19:      Cholesky                           true    Use Cholesky decomposition?
19:      CholeskyMode                          0    Save/load integrals? 0 no, 1 save, -1 load
19:      CholeskyNAFThr                0.000e+00    Cholesky natural auxiliary function threshold
19:      CholeskyShThr                 1.000e-02    Cholesky cache threshold
19:      CholeskyThr                   1.000e-07    Cholesky decomposition threshold
19:      ConvThr                       1.000e-06    Orbital gradient convergence threshold
19:      DIISComb                          false    Combine alpha and beta errors in unrestricted calcs?
19:      DIISEps                       1.000e-01    Start mixing in DIIS when error is
19:      DIISOrder                            10    How many DIIS iterations to keep in memory?
19:      DIISThr                       1.000e-02    DIIS error threshold for DIIS updates
19:      DecFock                           false    Use decontracted basis to calculate Fock matrix (direct HF)
19:      Decontract                                 Indices of atoms to decontract basis set for
19:      DensityFitting                    false    Use density fitting / RI?
19:      DimerSymmetry                     false    Do special calculation on dimer along z axis
19:      Direct                            false    Calculate two-electron integrals (or density fitting) on-the-fly?
19:      EField                      0.0 0.0 0.0    Electric field
19:      FittingBasis                       Auto    Basis to use for density fitting / RI (Auto for automatic)
19:      FittingMemory                      1000    Amount of memory in MB to use for exchange fitting
19:      FittingThreshold              1.000e-08    Linear dependence threshold for Coulomb integrals in density fitting
19:      ForcePol                          false    Force polarized calculation
19:      Guess                              Core    Used guess: SAD (default), NO, core, or GWH
19:      InputBohr                         false    Use atomic units as input units instead of angstrom?
19:      IntegralThresh                1.000e-14    Integral screening threshold
19:      LoadChk                                    File to load old results from
19:      Logfile                       Ne_dz.log    File to print out full information, stdout for screen
19:      MaxIter                             100    Maximum number of iterations in SCF cycle
19:      Method                               HF    Method used in calculation (HF or a DFT functional)
19:      Multiplicity                          1    Spin multiplicity
19:      Occupancies                                Orbital occupancies
19:      OptLM                              true    If spherical harmonics used, use cartesian s and p functions?
19:      SaveChk                       Ne_dz.chk    File to use as checkpoint
19:      Shift                         0.000e+00    Level shift to use in Hartree
19:      StrictIntegrals                   false    Use strict integrals?
19:      System                           Ne.xyz    System as an xyz file
19:      TRRHminS                      9.750e-01    Trust-Region Roothaan-Hall minimal occupied orbital overlap
19:      UseADIIS                           true    Use ADIIS for Fock matrix interpolation?
19:      UseBroyden                        false    Use Broyden mixing of Fock matrices?
19:      UseDIIS                            true    Use Pulay's Direct Inversion in the Iterative Subspace?
19:      UseLM                              true    Use a spherical harmonics basis set by default?
19:      UseTRRH                           false    Use Trust-Region Roothaan-Hall?
19:      Verbose                            true    Verbose calculation?
19: 
19: 
19: Running restricted HF calculation.
19: iter                E         dE  RMS dens  MAX dens  DIIS err  titer (s)
1/4 Test #19: Ne_dz_chk ........................***Exception: SegFault  0.17 sec
test 20
    Start 20: Ne_dz

20: Test command: /usr/ports/science/erkale/work-parallel/.build/src/test/chkcompare_omp "Ne_dz.chk"
20: Environment variables: 
20:  ERKALE_REFDIR=/usr/ports/science/erkale/work-parallel/erkale-0927d8c/refdata
20: Test timeout computed to be: 10000000
20: Reference directory is set to "/usr/ports/science/erkale/work-parallel/erkale-0927d8c/refdata".
2/4 Test #20: Ne_dz ............................***Exception: SegFault  0.05 sec
test 21
    Start 21: Ne_dz_cart_chk

21: Test command: /usr/ports/science/erkale/work-parallel/.build/src/erkale_omp "/usr/ports/science/erkale/work-parallel/erkale-0927d8c/tests/Ne_dz_cart.run"
21: Environment variables: 
21:  ERKALE_SYSDIR=/usr/ports/science/erkale/work-parallel/erkale-0927d8c/tests/xyz
21:  ERKALE_LIBRARY=/usr/ports/science/erkale/work-parallel/erkale-0927d8c/basis
21: Test timeout computed to be: 10000000
21: ERKALE - HF/DFT from Hel, OpenMP version, running on 8 cores.
21: (c) Susi Lehtola, 2010-2016.
21: 
21: This program is free software; you can redistribute it and/or modify
21: it under the terms of the GNU General Public License as published by
21: the Free Software Foundation; either version 2 of the License, or
21: (at your option) any later version.
21: 
21: Running on host yv.noip.me.
21: 
21: Current time is Thu 22 Nov 2018 09:17:24.
21: 
21: Current Settings used by ERKALE:
21:      AtomGuess                          Auto    Method used for atomic guess (Auto for same as method)
21:      Basis                           cc-pVDZ    Basis set used in calculation
21:      BasisCutoff                   1.000e-08    Cutoff for dropping out small primitives from contraction
21:      BasisOrth                          Auto    Method of orthonormalization of basis set
21:      BasisRotate                       false    Rotate basis set to remove redundant functions?
21:      Charge                                0    Total charge of system
21:      Cholesky                           true    Use Cholesky decomposition?
21:      CholeskyMode                          0    Save/load integrals? 0 no, 1 save, -1 load
21:      CholeskyNAFThr                0.000e+00    Cholesky natural auxiliary function threshold
21:      CholeskyShThr                 1.000e-02    Cholesky cache threshold
21:      CholeskyThr                   1.000e-07    Cholesky decomposition threshold
21:      ConvThr                       1.000e-06    Orbital gradient convergence threshold
21:      DIISComb                          false    Combine alpha and beta errors in unrestricted calcs?
21:      DIISEps                       1.000e-01    Start mixing in DIIS when error is
21:      DIISOrder                            10    How many DIIS iterations to keep in memory?
21:      DIISThr                       1.000e-02    DIIS error threshold for DIIS updates
21:      DecFock                           false    Use decontracted basis to calculate Fock matrix (direct HF)
21:      Decontract                                 Indices of atoms to decontract basis set for
21:      DensityFitting                    false    Use density fitting / RI?
21:      DimerSymmetry                     false    Do special calculation on dimer along z axis
21:      Direct                            false    Calculate two-electron integrals (or density fitting) on-the-fly?
21:      EField                      0.0 0.0 0.0    Electric field
21:      FittingBasis                       Auto    Basis to use for density fitting / RI (Auto for automatic)
21:      FittingMemory                      1000    Amount of memory in MB to use for exchange fitting
21:      FittingThreshold              1.000e-08    Linear dependence threshold for Coulomb integrals in density fitting
21:      ForcePol                          false    Force polarized calculation
21:      Guess                              Core    Used guess: SAD (default), NO, core, or GWH
21:      InputBohr                         false    Use atomic units as input units instead of angstrom?
21:      IntegralThresh                1.000e-14    Integral screening threshold
21:      LoadChk                                    File to load old results from
21:      Logfile                  Ne_dz_cart.log    File to print out full information, stdout for screen
21:      MaxIter                             100    Maximum number of iterations in SCF cycle
21:      Method                               HF    Method used in calculation (HF or a DFT functional)
21:      Multiplicity                          1    Spin multiplicity
21:      Occupancies                                Orbital occupancies
21:      OptLM                              true    If spherical harmonics used, use cartesian s and p functions?
21:      SaveChk                  Ne_dz_cart.chk    File to use as checkpoint
21:      Shift                         0.000e+00    Level shift to use in Hartree
21:      StrictIntegrals                   false    Use strict integrals?
21:      System                           Ne.xyz    System as an xyz file
21:      TRRHminS                      9.750e-01    Trust-Region Roothaan-Hall minimal occupied orbital overlap
21:      UseADIIS                           true    Use ADIIS for Fock matrix interpolation?
21:      UseBroyden                        false    Use Broyden mixing of Fock matrices?
21:      UseDIIS                            true    Use Pulay's Direct Inversion in the Iterative Subspace?
21:      UseLM                             false    Use a spherical harmonics basis set by default?
21:      UseTRRH                           false    Use Trust-Region Roothaan-Hall?
21:      Verbose                            true    Verbose calculation?
21: 
21: 
21: Running restricted HF calculation.
21: iter                E         dE  RMS dens  MAX dens  DIIS err  titer (s)
3/4 Test #21: Ne_dz_cart_chk ...................***Exception: SegFault  0.16 sec
test 22
    Start 22: Ne_dz_cart

22: Test command: /usr/ports/science/erkale/work-parallel/.build/src/test/chkcompare_omp "Ne_dz_cart.chk"
22: Environment variables: 
22:  ERKALE_REFDIR=/usr/ports/science/erkale/work-parallel/erkale-0927d8c/refdata
22: Test timeout computed to be: 10000000
22: Reference directory is set to "/usr/ports/science/erkale/work-parallel/erkale-0927d8c/refdata".
22: Total energy difference 1.284889e+02
4/4 Test #22: Ne_dz_cart .......................***Exception: Child aborted  0.02 sec

0% tests passed, 4 tests failed out of 4

Total Test time (real) =   0.41 sec

The following tests FAILED:
     19 - Ne_dz_chk (SEGFAULT)
     20 - Ne_dz (SEGFAULT)
     21 - Ne_dz_cart_chk (SEGFAULT)
     22 - Ne_dz_cart (Child aborted)
Errors while running CTest
$ ctest -V -R basictests
UpdateCTestConfiguration  from :/usr/ports/science/erkale/work-parallel/.build/DartConfiguration.tcl
UpdateCTestConfiguration  from :/usr/ports/science/erkale/work-parallel/.build/DartConfiguration.tcl
Test project /usr/ports/science/erkale/work-parallel/.build
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
    Start 1: build_basictests

1: Test command: /usr/local/bin/cmake "--build" "/usr/ports/science/erkale/work-parallel/.build" "--target" "basictests"
1: Test timeout computed to be: 10000000
1: /usr/local/bin/cmake -H/usr/ports/science/erkale/work-parallel/erkale-0927d8c -B/usr/ports/science/erkale/work-parallel/.build --check-build-system CMakeFiles/Makefile.cmake 0
1: /usr/local/bin/gmake -f CMakeFiles/Makefile2 basictests
1: gmake[1]: Entering directory '/usr/ports/science/erkale/work-parallel/.build'
1: /usr/local/bin/cmake -H/usr/ports/science/erkale/work-parallel/erkale-0927d8c -B/usr/ports/science/erkale/work-parallel/.build --check-build-system CMakeFiles/Makefile.cmake 0
1: /usr/local/bin/cmake -E cmake_progress_start /usr/ports/science/erkale/work-parallel/.build/CMakeFiles 59
1: /usr/local/bin/gmake -f CMakeFiles/Makefile2 src/test/CMakeFiles/basictests.dir/all
1: gmake[2]: Entering directory '/usr/ports/science/erkale/work-parallel/.build'
1: /usr/local/bin/gmake -f src/CMakeFiles/eriworker_gentransform.dir/build.make src/CMakeFiles/eriworker_gentransform.dir/depend
1: gmake[3]: Entering directory '/usr/ports/science/erkale/work-parallel/.build'
1: cd /usr/ports/science/erkale/work-parallel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /usr/ports/science/erkale/work-parallel/erkale-0927d8c /usr/ports/science/erkale/work-parallel/erkale-0927d8c/src /usr/ports/science/erkale/work-parallel/.build /usr/ports/science/erkale/work-parallel/.build/src /usr/ports/science/erkale/work-parallel/.build/src/CMakeFiles/eriworker_gentransform.dir/DependInfo.cmake --color=
1: gmake[3]: Leaving directory '/usr/ports/science/erkale/work-parallel/.build'
1: /usr/local/bin/gmake -f src/CMakeFiles/eriworker_gentransform.dir/build.make src/CMakeFiles/eriworker_gentransform.dir/build
1: gmake[3]: Entering directory '/usr/ports/science/erkale/work-parallel/.build'
1: gmake[3]: Nothing to be done for 'src/CMakeFiles/eriworker_gentransform.dir/build'.
1: gmake[3]: Leaving directory '/usr/ports/science/erkale/work-parallel/.build'
1: [  5%] Built target eriworker_gentransform
1: /usr/local/bin/gmake -f src/CMakeFiles/liberkale.dir/build.make src/CMakeFiles/liberkale.dir/depend
1: gmake[3]: Entering directory '/usr/ports/science/erkale/work-parallel/.build'
1: cd /usr/ports/science/erkale/work-parallel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /usr/ports/science/erkale/work-parallel/erkale-0927d8c /usr/ports/science/erkale/work-parallel/erkale-0927d8c/src /usr/ports/science/erkale/work-parallel/.build /usr/ports/science/erkale/work-parallel/.build/src /usr/ports/science/erkale/work-parallel/.build/src/CMakeFiles/liberkale.dir/DependInfo.cmake --color=
1: gmake[3]: Leaving directory '/usr/ports/science/erkale/work-parallel/.build'
1: /usr/local/bin/gmake -f src/CMakeFiles/liberkale.dir/build.make src/CMakeFiles/liberkale.dir/build
1: gmake[3]: Entering directory '/usr/ports/science/erkale/work-parallel/.build'
1: gmake[3]: Nothing to be done for 'src/CMakeFiles/liberkale.dir/build'.
1: gmake[3]: Leaving directory '/usr/ports/science/erkale/work-parallel/.build'
1: [ 88%] Built target liberkale
1: /usr/local/bin/gmake -f src/emd/CMakeFiles/liberkale_emd.dir/build.make src/emd/CMakeFiles/liberkale_emd.dir/depend
1: gmake[3]: Entering directory '/usr/ports/science/erkale/work-parallel/.build'
1: cd /usr/ports/science/erkale/work-parallel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /usr/ports/science/erkale/work-parallel/erkale-0927d8c /usr/ports/science/erkale/work-parallel/erkale-0927d8c/src/emd /usr/ports/science/erkale/work-parallel/.build /usr/ports/science/erkale/work-parallel/.build/src/emd /usr/ports/science/erkale/work-parallel/.build/src/emd/CMakeFiles/liberkale_emd.dir/DependInfo.cmake --color=
1: gmake[3]: Leaving directory '/usr/ports/science/erkale/work-parallel/.build'
1: /usr/local/bin/gmake -f src/emd/CMakeFiles/liberkale_emd.dir/build.make src/emd/CMakeFiles/liberkale_emd.dir/build
1: gmake[3]: Entering directory '/usr/ports/science/erkale/work-parallel/.build'
1: gmake[3]: Nothing to be done for 'src/emd/CMakeFiles/liberkale_emd.dir/build'.
1: gmake[3]: Leaving directory '/usr/ports/science/erkale/work-parallel/.build'
1: [ 98%] Built target liberkale_emd
1: /usr/local/bin/gmake -f src/test/CMakeFiles/basictests.dir/build.make src/test/CMakeFiles/basictests.dir/depend
1: gmake[3]: Entering directory '/usr/ports/science/erkale/work-parallel/.build'
1: cd /usr/ports/science/erkale/work-parallel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /usr/ports/science/erkale/work-parallel/erkale-0927d8c /usr/ports/science/erkale/work-parallel/erkale-0927d8c/src/test /usr/ports/science/erkale/work-parallel/.build /usr/ports/science/erkale/work-parallel/.build/src/test /usr/ports/science/erkale/work-parallel/.build/src/test/CMakeFiles/basictests.dir/DependInfo.cmake --color=
1: gmake[3]: Leaving directory '/usr/ports/science/erkale/work-parallel/.build'
1: /usr/local/bin/gmake -f src/test/CMakeFiles/basictests.dir/build.make src/test/CMakeFiles/basictests.dir/build
1: gmake[3]: Entering directory '/usr/ports/science/erkale/work-parallel/.build'
1: gmake[3]: Nothing to be done for 'src/test/CMakeFiles/basictests.dir/build'.
1: gmake[3]: Leaving directory '/usr/ports/science/erkale/work-parallel/.build'
1: [100%] Built target basictests
1: gmake[2]: Leaving directory '/usr/ports/science/erkale/work-parallel/.build'
1: /usr/local/bin/cmake -E cmake_progress_start /usr/ports/science/erkale/work-parallel/.build/CMakeFiles 0
1: gmake[1]: Leaving directory '/usr/ports/science/erkale/work-parallel/.build'
1/2 Test #1: build_basictests .................   Passed    0.85 sec
test 2
    Start 2: basictests

2: Test command: /usr/ports/science/erkale/work-parallel/.build/src/test/basictests_omp
2: Test timeout computed to be: 10000000
2: Indices OK.
2: Solid harmonics OK.
2: Checkpointing OK.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Bad memory unallocation! :    2  0x0
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is Terminated. Because you tried to allocate too many memory regions.
2: BLAS : Program is 
2/2 Test #2: basictests .......................***Exception: SegFault  0.96 sec

The following tests passed:
    build_basictests

50% tests passed, 1 tests failed out of 2

Total Test time (real) =   1.82 sec

The following tests FAILED:
      2 - basictests (SEGFAULT)
Errors while running CTest
susilehtola commented 5 years ago

OK so your BLAS is broken,. Not a problem in ERKALE.

yurivict commented 5 years ago

Wait, what about the failure of water_dimer_tpssh_xch in sequential case? It isn't linked with OpenBlas at all.

susilehtola commented 5 years ago

1) make sure you have the newest revision 2) do a clean rebuild in a new object directory

The error is basically that the checkpoint file is corrupt, and since the XRS program checks if a previous calculation exists it will use it, it probably hasn't run the calculation at all.

yurivict commented 5 years ago

It was indeed the problem in OpenBLAS that it limited the number of threads to 16. Now I have it increased to 128.

But water_dimer_wb97x_fch.run still fails with this exception: Cannot recognize keyword XRSMethod!

Also, this exception is thrown at src/settings.cpp:505 but is never caught, and eventually causes the program to abort. Do you know which catch statement is supposed to catch this exception? I see that the line set.parse(std::string(argv[1]),true); in src/main.cpp is already a main function and has no catch statement. So it appears that this exception is always thrown out into the main function, which always leads to SIGABRT and its message is never printed.

rev. 0927d8c

susilehtola commented 5 years ago

Run ctest like I told you to, since you're not running water_dimer_wb97x_fch the way it is supposed to be run. It has to be run with erkale_xrs not erkale, like the other _{xrs,fch,xch} test cases.

yurivict commented 5 years ago 
[x@x /usr/ports/science/erkale/work-parallel/.build] $ ctest -VV -R water_dimer_wb97x_fch
UpdateCTestConfiguration  from :/usr/ports/science/erkale/work-parallel/.build/DartConfiguration.tcl
UpdateCTestConfiguration  from :/usr/ports/science/erkale/work-parallel/.build/DartConfiguration.tcl
Test project /usr/ports/science/erkale/work-parallel/.build
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 143
    Start 143: water_dimer_wb97x_fch_chk

143: Test command: /usr/ports/science/erkale/work-parallel/.build/src/xrs/erkale_xrs_omp "/usr/ports/science/erkale/work-parallel/erkale-0927d8c/tests/water_dimer_wb97x_fch.run"
143: Environment variables: 
143:  ERKALE_SYSDIR=/usr/ports/science/erkale/work-parallel/erkale-0927d8c/tests/xyz
143:  ERKALE_LIBRARY=/usr/ports/science/erkale/work-parallel/erkale-0927d8c/basis
143: Test timeout computed to be: 10000000
143: ERKALE - XRS from Hel, OpenMP version, running on 8 cores.
143: (c) Susi Lehtola, 2010-2016.
143: 
143: This program is free software; you can redistribute it and/or modify
143: it under the terms of the GNU General Public License as published by
143: the Free Software Foundation; either version 2 of the License, or
143: (at your option) any later version.
143: 
143: Running on host yv.noip.me.
143: 
143: Current time is Fri 23 Nov 2018 08:00:42.
143: 
143: No converged calculation found in SaveChk.
1/2 Test #143: water_dimer_wb97x_fch_chk ........***Exception: Child aborted  0.04 sec
test 144
    Start 144: water_dimer_wb97x_fch

144: Test command: /usr/ports/science/erkale/work-parallel/.build/src/test/chkcompare_omp "water_dimer_wb97x_fch.chk"
144: Environment variables: 
144:  ERKALE_REFDIR=/usr/ports/science/erkale/work-parallel/erkale-0927d8c/refdata
144: Test timeout computed to be: 10000000
144: Reference directory is set to "/usr/ports/science/erkale/work-parallel/erkale-0927d8c/refdata".
2/2 Test #144: water_dimer_wb97x_fch ............***Exception: Child aborted  0.01 sec

0% tests passed, 2 tests failed out of 2

Total Test time (real) =   0.06 sec

The following tests FAILED:
    143 - water_dimer_wb97x_fch_chk (Child aborted)
    144 - water_dimer_wb97x_fch (Child aborted)
Errors while running CTest
susilehtola commented 5 years ago

... and was the object directory clean like I asked you? Please follow the procedure I asked you yesterday.

yurivict commented 5 years ago

It is clean. This is the first test run there.

susilehtola commented 5 years ago

Umm, that makes no sense - you have to run water_dimer_wb97x first, like the test suite does.

Like I said. Please run ctest a clean directory.