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SDSC: PKG - expanse/0.17.3/cpu/a - Missing VASP (example application) #45

Closed nwolter closed 1 year ago

mkandes commented 1 year ago

@nwolter - When you get a chance, can you please add the spack_cpu, spack_gpu, spack_dev_cpu, and spack_dev_gpu users to the vasp and vasp-6 groups?

nwolter commented 1 year ago

spack users added to vasp and vasp-6

mkandes commented 1 year ago

Confirmed.

[spack_cpu@login01 ~]$ groups
spack use300 gaussian vasp vasp-6
[spack_gpu@login01 ~]$ groups
spack use300 gaussian vasp vasp-6
[spack_dev_cpu@login01 ~]$ groups
spack_dev use300 gaussian vasp vasp-6
[spack_dev_gpu@login01 ~]$ groups
spack_dev use300 gaussian vasp vasp-6
mkandes commented 1 year ago

@nwolter - First install of vasp6 ready-for-testing.

[mkandes_test@login02]~% module spider vasp6

----------------------------------------------------------------------------
  vasp6/6.2.1: vasp6/6.2.1/3fjhwod
----------------------------------------------------------------------------

    You will need to load all module(s) on any one of the lines below before the "vasp6/6.2.1/3fjhwod" module is available to load.

      gcc/10.2.0/npcyll4  openmpi/4.1.3/4ejofw7

[mkandes_test@login02]~% module load vasp6/6.2.1
Lmod has detected the following error:  Unable to load module
because of error when evaluating modulefile:

/cm/shared/apps/spack/0.17.3/cpu/a/share/spack/lmod/linux-rocky8-x86_64/openmpi/4.1.3-4ejofw7/gcc/10.2.0/vasp6/6.2.1/3fjhwod.lua:
Empty or non-existant file
     Please check the modulefile and especially if there is a the line number
specified in the above message 
While processing the following module(s):
    Module fullname      Module Filename
    ---------------      ---------------
    vasp6/6.2.1/3fjhwod  /cm/shared/apps/spack/0.17.3/cpu/a/share/spack/lmod/linux-rocky8-x86_64/openmpi/4.1.3-4ejofw7/gcc/10.2.0/vasp6/6.2.1/3fjhwod.lua

[mkandes_test@login02]~%
mkandes commented 1 year ago

aocc version also ready for testing

[mkandes@login01 ~]$ module spider vasp6/6.2.1/i2wqw25

----------------------------------------------------------------------------
  vasp6/6.2.1: vasp6/6.2.1/i2wqw25
----------------------------------------------------------------------------

    You will need to load all module(s) on any one of the lines below before the "vasp6/6.2.1/i2wqw25" module is available to load.

      aocc/3.2.0/io3s466  openmpi/4.1.3/6bxpzag

    Help:
       The Vienna Ab initio Simulation Package (VASP) is a computer program
      for atomic scale materials modelling, e.g. electronic structure
      calculations and quantum-mechanical molecular dynamics, from first
      principles.

[mkandes@login01 ~]$
nwolter commented 1 year ago

Something strange seems to have happened to VASP module I was testing. Initial test with gcc went well, but I can no longer see the gcc or aocc module listed above when using spider command. Can someone set me straight.

mkandes commented 1 year ago

@nwolter - My guess is your ~/.lmod.d cache is the source of the confusion. You can simply remove it and you'll should see the original behavior. But even with it in place, you should still be able to access the new modules too. 

[nickel@login01 ~]$ module spider vasp

----------------------------------------------------------------------------
  vasp:
----------------------------------------------------------------------------
     Versions:
        vasp/5.4.4-openblas-wannier90
        vasp/5.4.4-openblas
        vasp/5.4.4-vaspsol
        vasp/5.4.4-vtst-openblas
        vasp/5.4.4
        vasp/6.1.1-openblas
        vasp/6.1.1-vaspsol
        vasp/6.1.1-vtst-openblas
        vasp/6.2.1
     Other possible modules matches:
        vasp6/6.2.1

----------------------------------------------------------------------------
  To find other possible module matches execute:

      $ module -r spider '.*vasp.*'

----------------------------------------------------------------------------
[nickel@login01 ~]$ module spider vasp6/6.2.1

----------------------------------------------------------------------------
  vasp6/6.2.1:
----------------------------------------------------------------------------
     Versions:
        vasp6/6.2.1/i2wqw25
        vasp6/6.2.1/3fjhwod

----------------------------------------------------------------------------
  For detailed information about a specific "vasp6/6.2.1" package (including how to load the modules) use the module's full name. Note that names that have a trailing (E) are extensions provided by other modules.
  For example:

     $ module spider vasp6/6.2.1/3fjhwod
----------------------------------------------------------------------------

[nickel@login01 ~]$ module spider vasp6/6.2.1/3fjhwod

----------------------------------------------------------------------------
  vasp6/6.2.1: vasp6/6.2.1/3fjhwod
----------------------------------------------------------------------------

    You will need to load all module(s) on any one of the lines below before the "vasp6/6.2.1/3fjhwod" module is available to load.

      gcc/10.2.0/npcyll4  openmpi/4.1.3/4ejofw7

    Help:
       The Vienna Ab initio Simulation Package (VASP) is a computer program
      for atomic scale materials modelling, e.g. electronic structure
      calculations and quantum-mechanical molecular dynamics, from first
      principles.

[nickel@login01 ~]$ module load gcc/10.2.0/npcyll4 
[nickel@login01 ~]$ module load openmpi/4.1.3      
openmpi/4.1.3          openmpi/4.1.3/4ejofw7  
[nickel@login01 ~]$ module load openmpi/4.1.3/4ejofw7 
[nickel@login01 ~]$ module load vasp6/6.2.1
[nickel@login01 ~]$ module list

Currently Loaded Modules:
  1) slurm/expanse/21.08.8   5) fftw/3.3.10/qogw3ss
  2) gcc/10.2.0/npcyll4      6) openblas/0.3.18/fgk2tlu
  3) ucx/1.10.1/kfriyyt      7) netlib-scalapack/2.1.0/yxq6bi4
  4) openmpi/4.1.3/4ejofw7   8) vasp6/6.2.1/3fjhwod

[nickel@login01 ~]$
nwolter commented 1 year ago

`Still no joy. What am I doing wrong? Its giving me the gpu version. 

[nickel@login01 ~]$ rm -rf ~/.lmod.d/
[nickel@login01 ~]$ module purge
[nickel@login01 ~]$ module use /cm/shared/apps/spack/0.17.3/cpu/a/share/spack/lmod/linux-rocky8-x86_64/Core
[nickel@login01 ~]$  module spider vasp/6.2.1

------------------------------------------------------------------------------------------------------------------------------------------------------------
  vasp: vasp/6.2.1
------------------------------------------------------------------------------------------------------------------------------------------------------------

    You will need to load all module(s) on any one of the lines below before the "vasp/6.2.1" module is available to load.

      gpu/0.15.4  intel/19.0.5.281  openmpi/4.0.4

    Help:
       The Vienna Ab initio Simulation Package (VASP) is a computer program
      for atomic scale materials modelling, e.g. electronic structure
      calculations and quantum-mechanical molecular dynamics, from first
      principles.
mkandes commented 1 year ago

@nwolter - You're simply looking for the 'wrong' package. The new VASP 6 packages are actually named 'vasp6' to help accommodate the version/group permissions.

[nickel@login01 ~]$ module purge
[nickel@login01 ~]$ module load slurm
[nickel@login01 ~]$ module use /cm/shared/apps/spack/0.17.3/cpu/a/share/spack/lmod/linux-rocky8-x86_64/Core
[nickel@login01 ~]$ module spider vasp6

----------------------------------------------------------------------------
  vasp6/6.2.1:
----------------------------------------------------------------------------
     Versions:
        vasp6/6.2.1/i2wqw25
        vasp6/6.2.1/3fjhwod

----------------------------------------------------------------------------
  For detailed information about a specific "vasp6/6.2.1" package (including how to load the modules) use the module's full name. Note that names that have a trailing (E) are extensions provided by other modules.
  For example:

     $ module spider vasp6/6.2.1/3fjhwod
----------------------------------------------------------------------------

[nickel@login01 ~]$ module spider vasp/6.2.1

----------------------------------------------------------------------------
  vasp: vasp/6.2.1
----------------------------------------------------------------------------

    You will need to load all module(s) on any one of the lines below before the "vasp/6.2.1" module is available to load.

      gpu/0.15.4  intel/19.0.5.281  openmpi/4.0.4

    Help:
       The Vienna Ab initio Simulation Package (VASP) is a computer program
      for atomic scale materials modelling, e.g. electronic structure
      calculations and quantum-mechanical molecular dynamics, from first
      principles.

[nickel@login01 ~]$
nwolter commented 1 year ago

Duh

nwolter commented 1 year ago

both aocc and gcc examples tested with the following tails for the two logs. ==> vasp6.2_gcc_21210892.log <== Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL

==> vasp6.2_aocc__21278160.log <== Warning: ieee_invalid is signaling Warning: ieee_divide_by_zero is signaling Warning: ieee_underflow is signaling Warning: ieee_inexact is signaling FORTRAN STOP Warning: ieee_invalid is si.......

mkandes commented 1 year ago

I think this is a 'known' issue. e.g., I may have made a note about it in the Expanse acceptance testing confluence page. But we can raise the issue at the meeting this Friday and check with Mahi and Jerry.

From: nwolter @.> Sent: Wednesday, March 22, 2023 11:43 AM To: sdsc/spack @.> Cc: Kandes, Martin @.>; Comment @.> Subject: Re: [sdsc/spack] SDSC: PKG - expanse/0.17.3/cpu/a - Missing VASP (example application) (Issue #45)

both aocc and gcc examples tested with the following tails for the two logs. ==> vasp6.2_gcc_21210892.log <== Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL

==> vasp6.2_aocc__21278160.log <== Warning: ieee_invalid is signaling Warning: ieee_divide_by_zero is signaling Warning: ieee_underflow is signaling Warning: ieee_inexact is signaling FORTRAN STOP Warning: ieee_invalid is si.......

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nwolter commented 1 year ago

Yes, according to Mahi it is a known issue, just wanted to note them in the issue report for completeness. Nicole

From: Marty Kandes @.> Sent: Wednesday, March 22, 2023 7:17 PM To: sdsc/spack @.> Cc: Wolter, Nicole @.>; Mention @.> Subject: Re: [sdsc/spack] SDSC: PKG - expanse/0.17.3/cpu/a - Missing VASP (example application) (Issue #45)

I think this is a 'known' issue. e.g., I may have made a note about it in the Expanse acceptance testing confluence page. But we can raise the issue at the meeting this Friday and check with Mahi and Jerry.

From: nwolter @.<mailto:@.>> Sent: Wednesday, March 22, 2023 11:43 AM To: sdsc/spack @.<mailto:@.>> Cc: Kandes, Martin @.<mailto:@.>>; Comment @.<mailto:@.>> Subject: Re: [sdsc/spack] SDSC: PKG - expanse/0.17.3/cpu/a - Missing VASP (example application) (Issue #45)

both aocc and gcc examples tested with the following tails for the two logs. ==> vasp6.2_gcc_21210892.log <== Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL

==> vasp6.2_aocc__21278160.log <== Warning: ieee_invalid is signaling Warning: ieee_divide_by_zero is signaling Warning: ieee_underflow is signaling Warning: ieee_inexact is signaling FORTRAN STOP Warning: ieee_invalid is si.......

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