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fix machine file for serial run on lawrencium-lr2 #169

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rgknox opened this issue Jan 5, 2017 · 1 comment
Closed

fix machine file for serial run on lawrencium-lr2 #169

rgknox opened this issue Jan 5, 2017 · 1 comment
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bug - software engineering

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@rgknox
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rgknox commented Jan 5, 2017

Summary of Issue:

lawrencium lr2 machine files have a bug in them that prevent serial runs. The issue is that mpirun arguments are passed to the execution string, when no mpirun command is issued. The case.run script ends up passing a system command which starts with '-np 1 ...' and of course the system does not know what to do.

The fix is trivial, as the execution arguments need to be removed for the serial case. It should mirror the lawrencium-lr3 entry.

Expected behavior and actual behavior:

Steps to reproduce the problem (should include create_newcase or create_test command along with any user_nl or xml changes):

What is the changeset ID of the code, and the machine you are using:

have you modified the code? If so, it must be committed and available for testing:

Screen output or output files showing the error message and context:
@rgknox rgknox mentioned this issue Jan 6, 2017
Merged
bandre-ucar added a commit that referenced this issue Feb 6, 2017
@bandre-ucar
Fixes to carbon accounting and lr2 machine files
cdb9db7 
Merge branch 'rgknox-leafnpp-diag-fix'

This pull request mostly deals with some bug fixes to carbon
accounting. @jenniferholm noticed that the diagnostics for leaf_npp
were periodically showing negative values. Through #164 we identified
that this occurred because daily carbon balances during the allocation
sequences were sometimes negative to to high respiration and low
gpp. The model was correctly using storage carbon to "pay" the
negative daily carbon balance and allow maintenance respiration to
occur, it was not however correctly diagnosing this flow. The
accounting of this process is a little complicated because storage can
be used to pay for maintenance respiration as well as maintenance
turnover demand.

During the process of verifying that carbon accounting errors were
low, I triggered spurious values of output variables that triggered
netcdf write errors, this lead to the identification that
cohort%npp_accum was not being properly copied during copying of
cohorts during patch fission.

A fix was needed to lawrencium machine files for its lr2 partition for
serial runs. While these changes are unrelated to carbon accounting,
they are trivial and simple, so I bundled them here.

Fixes: #164, #169, #168 and possibly #154

User interface changes?: no

Code review: requesting @jenniferholm and @serbinsh for evaluation in
their science algorithms.

Testing:
  rgknox:
    Test suite: lawrencium lr3 (baseline) and lawrencium-lr2 (non-baseline) edTest, Rapid Science Check tool (single site multi-decadal analysis)
    Test baseline: 5c5928f
    Test namelist changes: none
    Test answer changes:
    Test summary: all PASS

  andre:
    Test suite: ed - yellowstone gnu, intel, pgi
                     hobart nag
    Test baseline: 30f84d7
    Test namelist changes: none
    Test answer changes: bit for bit
    Test summary: all tests pass

    Test suite: clm_short - yellowstone gnu, intel, pgi
    Test baseline: clm4_5_12_r195
    Test namelist changes: none
    Test answer changes: bit for bit
    Test summary: all tests pass
@rgknox
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rgknox commented Mar 1, 2017

this was fixed via: 4009321

@rgknox rgknox closed this as completed Mar 1, 2017
rgknox pushed a commit that referenced this issue Apr 21, 2017
@bandre-ucar
Fixes to carbon accounting and lr2 machine files
159ae98 
Merge branch 'rgknox-leafnpp-diag-fix'

This pull request mostly deals with some bug fixes to carbon
accounting. @jenniferholm noticed that the diagnostics for leaf_npp
were periodically showing negative values. Through #164 we identified
that this occurred because daily carbon balances during the allocation
sequences were sometimes negative to to high respiration and low
gpp. The model was correctly using storage carbon to "pay" the
negative daily carbon balance and allow maintenance respiration to
occur, it was not however correctly diagnosing this flow. The
accounting of this process is a little complicated because storage can
be used to pay for maintenance respiration as well as maintenance
turnover demand.

During the process of verifying that carbon accounting errors were
low, I triggered spurious values of output variables that triggered
netcdf write errors, this lead to the identification that
cohort%npp_accum was not being properly copied during copying of
cohorts during patch fission.

A fix was needed to lawrencium machine files for its lr2 partition for
serial runs. While these changes are unrelated to carbon accounting,
they are trivial and simple, so I bundled them here.

Fixes: #164, #169, #168 and possibly #154

User interface changes?: no

Code review: requesting @jenniferholm and @serbinsh for evaluation in
their science algorithms.

Testing:
  rgknox:
    Test suite: lawrencium lr3 (baseline) and lawrencium-lr2 (non-baseline) edTest, Rapid Science Check tool (single site multi-decadal analysis)
    Test baseline: 5c5928f
    Test namelist changes: none
    Test answer changes:
    Test summary: all PASS

  andre:
    Test suite: ed - yellowstone gnu, intel, pgi
                     hobart nag
    Test baseline: 30f84d7
    Test namelist changes: none
    Test answer changes: bit for bit
    Test summary: all tests pass

    Test suite: clm_short - yellowstone gnu, intel, pgi
    Test baseline: clm4_5_12_r195
    Test namelist changes: none
    Test answer changes: bit for bit
    Test summary: all tests pass
rgknox pushed a commit that referenced this issue May 23, 2017
@bandre-ucar
Fixes to carbon accounting and lr2 machine files
ac0a2a5 
Merge branch 'rgknox-leafnpp-diag-fix'

This pull request mostly deals with some bug fixes to carbon
accounting. @jenniferholm noticed that the diagnostics for leaf_npp
were periodically showing negative values. Through #164 we identified
that this occurred because daily carbon balances during the allocation
sequences were sometimes negative to to high respiration and low
gpp. The model was correctly using storage carbon to "pay" the
negative daily carbon balance and allow maintenance respiration to
occur, it was not however correctly diagnosing this flow. The
accounting of this process is a little complicated because storage can
be used to pay for maintenance respiration as well as maintenance
turnover demand.

During the process of verifying that carbon accounting errors were
low, I triggered spurious values of output variables that triggered
netcdf write errors, this lead to the identification that
cohort%npp_accum was not being properly copied during copying of
cohorts during patch fission.

A fix was needed to lawrencium machine files for its lr2 partition for
serial runs. While these changes are unrelated to carbon accounting,
they are trivial and simple, so I bundled them here.

Fixes: #164, #169, #168 and possibly #154

User interface changes?: no

Code review: requesting @jenniferholm and @serbinsh for evaluation in
their science algorithms.

Testing:
  rgknox:
    Test suite: lawrencium lr3 (baseline) and lawrencium-lr2 (non-baseline) edTest, Rapid Science Check tool (single site multi-decadal analysis)
    Test baseline: 5c5928f
    Test namelist changes: none
    Test answer changes:
    Test summary: all PASS

  andre:
    Test suite: ed - yellowstone gnu, intel, pgi
                     hobart nag
    Test baseline: 30f84d7
    Test namelist changes: none
    Test answer changes: bit for bit
    Test summary: all tests pass

    Test suite: clm_short - yellowstone gnu, intel, pgi
    Test baseline: clm4_5_12_r195
    Test namelist changes: none
    Test answer changes: bit for bit
    Test summary: all tests pass
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