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Change (make flexible) placement of loadR.sh in sbatch_master #10

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smjenness opened this issue Aug 5, 2020 · 17 comments
Open

Change (make flexible) placement of loadR.sh in sbatch_master #10

smjenness opened this issue Aug 5, 2020 · 17 comments
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@smjenness

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@smjenness
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smjenness commented Aug 5, 2020 •
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cc: @AdrienLeGuillou

After that, change Hyak instructions on https://github.com/statnet/computing/tree/master/slurmLite

after that, address wiki issue here: statnet/computing#6
@smjenness smjenness self-assigned this Aug 5, 2020
@AdrienLeGuillou
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as we discussed, I changed

#!/bin/bash

. /gscratch/csde/spack/spack/share/spack/setup-env.sh
module load r-4.0.0-gcc-9.2.0-p7wezul

to

#!/bin/bash

. /gscratch/csde/spack/spack/share/spack/setup-env.sh
spack load [email protected]

and it gives me the following error:

==> Error: No compilers for operating system centos7 satisfy spec [email protected]

is there something I am doing differently than you?

@smjenness
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Hmm... no I think it is the same. After you run setup-env can you do: spack find and report the results here.

@AdrienLeGuillou
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I get this:

[aleguil@mox1 ~]$ . /gscratch/csde/spack/spack/share/spack/setup-env.sh
[aleguil@mox1 ~]$ spack find
==> 170 installed packages
-- linux-centos7-broadwell / [email protected] --------------------------
[email protected]      [email protected]                   [email protected]     [email protected]
[email protected]      [email protected]              [email protected]     [email protected]
[email protected]      [email protected]                [email protected]     [email protected]
[email protected]    [email protected]                [email protected]      [email protected]
[email protected]    [email protected]                   [email protected]      [email protected]
[email protected]    [email protected]                   [email protected]     [email protected]
[email protected]     [email protected]                   [email protected]     [email protected]
[email protected]     [email protected]  [email protected]      [email protected]
[email protected]        [email protected]  [email protected]      [email protected]
[email protected]        [email protected]  [email protected]     [email protected]
[email protected]        [email protected]                   [email protected]          [email protected]
[email protected]       [email protected]                     [email protected]          [email protected]
[email protected]       [email protected]                [email protected]       [email protected]
[email protected]       [email protected]                [email protected]       [email protected]
[email protected]       [email protected]                [email protected]    [email protected]
[email protected]       [email protected]               [email protected]    [email protected]
[email protected]       [email protected]              [email protected]  [email protected]
[email protected]        [email protected]              [email protected]  [email protected]
[email protected]        [email protected]                    [email protected]       [email protected]
[email protected]        [email protected]                    [email protected]        [email protected]
[email protected]      [email protected]                  [email protected]        [email protected]
[email protected]      [email protected]                 [email protected]       [email protected]
[email protected]        [email protected]                  [email protected]     [email protected]
[email protected]        [email protected]                    [email protected]     [email protected]
[email protected]    [email protected]              [email protected]     [email protected]
[email protected]         [email protected]                 [email protected]     [email protected]
[email protected]    [email protected]                 [email protected]       [email protected]
[email protected]  [email protected]           [email protected]       [email protected]
[email protected]  [email protected]           [email protected]       [email protected]
[email protected]  [email protected]           [email protected]          [email protected]
[email protected]   [email protected]                 [email protected]          [email protected]
[email protected]     [email protected]                 [email protected]          [email protected]
[email protected]    [email protected]               [email protected]
[email protected]        [email protected]               [email protected]

-- linux-centos7-haswell / [email protected] ----------------------------
[email protected]              [email protected]  [email protected]                 [email protected]
[email protected]            [email protected]        [email protected]                  [email protected]
[email protected]                [email protected]         lua-luafilesystem@1_7_0_2  [email protected]
[email protected]                [email protected]          [email protected]        [email protected]
[email protected]              [email protected]      [email protected]                  [email protected]
[email protected]  [email protected]     [email protected]                  [email protected]
[email protected]                [email protected]   [email protected]                 [email protected]
[email protected]                  [email protected]     [email protected]                [email protected]
[email protected]                [email protected]     [email protected]             [email protected]

[email protected] is present but I still get the error

==> Error: No compilers for operating system centos7 satisfy spec [email protected]

@smjenness
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Can you restart your session, load spack, and then run spack compiler find. Then try spack load

@AdrienLeGuillou
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[aleguil@mox1 ~]$ . /gscratch/csde/spack/spack/share/spack/setup-env.sh
[aleguil@mox1 ~]$ spack compiler find
==> Found no new compilers
==> Compilers are defined in the following files:
    /usr/lusers/aleguil/.spack/linux/compilers.yaml
[aleguil@mox1 ~]$ spack load [email protected]
==> Error: No compilers for operating system centos7 satisfy spec [email protected]

@smjenness
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what do you have listed here: ~/.spack/linux/compilers.yaml

@AdrienLeGuillou
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I was actually looking into it:

compilers:
- compiler:
    paths:
      cc: /usr/bin/gcc
      cxx: /usr/bin/g++
      f77: /usr/bin/gfortran
      fc: /usr/bin/gfortran
    operating_system: centos7
    target: x86_64
    modules: []
    environment:
      unset: []
    extra_rpaths: []
    flags: {}
    spec: [email protected]

@smjenness
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ok try this: spack load [email protected], spack compiler find (this should add 9.2.0 to your .yaml), restart session, load spack, spack load [email protected]

@AdrienLeGuillou
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does not work either.

[aleguil@mox1 linux]$ spack load [email protected]
[aleguil@mox1 linux]$ spack load [email protected]
==> Error: No compilers for operating system centos7 satisfy spec [email protected]

I think I need to do

spack find <path to gcc 9.2>

to register it

@smjenness
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wait, did you do spack compiler find after spack load [email protected]?

@AdrienLeGuillou
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no, just spack load [email protected]

@smjenness
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try this sequence, as suggested above:
spack load [email protected], spack compiler find (this should add 9.2.0 to your .yaml), restart session, load spack, spack load [email protected]

@AdrienLeGuillou
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my bad, I read to fast.

It worked this time.

@smjenness
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smjenness commented Aug 13, 2020 •
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excellent, can you add this step to any instructions on statnet/computing?
I had it listed here, but this is out of date, and pertains to building GCC and R (mostly for me): https://github.com/statnet/computing/wiki/Build-Hyak-Stack-from-Scratch-with-Spack
anything that lists using spack load needs to include this step of updating the compiler yaml with spack compiler find

@AdrienLeGuillou
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On it, where on the repo do you want me to put that info?

  • wiki? Build-Hyak-Stack-from-Scratch-with-Spack?
  • reproducible env readme?
  • other

@smjenness
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I was thinking somewhere on this readme: https://github.com/statnet/computing/tree/master/build

@AdrienLeGuillou
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I updated the "loadR.sh" file in "build" and added an explanation on how to correct the missing compiler error.

I also modified the "reproducible env" README saying that "loadR.sh" should be copied in the project's folder. I made linked to the "build" README so the user can know where to look

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