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WIP: various fixes #223

Merged
merged 11 commits into from Feb 13, 2017
Merged

WIP: various fixes #223

merged 11 commits into from Feb 13, 2017

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stgeke
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@stgeke stgeke commented Feb 12, 2017

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- Delete compile test as the executables may work on the compute node only
- Move stdout to the corresponding .re2 routines
- Make deformed elements the default
Exit makenek if any subcommands return a non-zero status
Output <casename>.his instead of hpts.out
Make sure we always loop over nelt in fix_geom
Delete old history point routines
Do not bail out if we evaluate compiler for MPI wrapper
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stgeke commented Feb 12, 2017

@RonRahaman It looks like the Pyhton scripts parse the makefile created by makenek. This PR changes some variable names like F77->FC, P->FFLAGS, lFLAGS->LDFLAGS. I guess that's why the regression test fail. What do you think?

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@stgeke, yes, that would be the reason. I can make a fix to NekTests.py then submit a PR to stgeke:master. After you approve that PR, the changes will appear here. Does that sound okay?

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I have a fix for the issue in nekTests.py, but it exposed this issue with makenek.inc. If I omit the -s flag, the tests succeed. How do you want to fix makenek.inc?

core/makenek.inc Outdated
if [ $? -ne 0 ]; then
echo "FATAL ERROR: Cannot find $F77!"
# test if F77 compiler exists
if ! which -s `echo $F77 | awk '{print $1}'` ; then
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The -s option is valid for the which command in whatever flavor of BSD UNIX that Mac OS/X uses. It is NOT valid for the flavor of GNU/Linux that Ubuntu and Debian use. This will cause the if statement to fail and makenek to exit with the "FATAL ERROR: Cannot find .." error.

This is what man which shows on my Ubuntu workstation:

WHICH(1)                                                                                                              General Commands Manual                                                                                                             WHICH(1)

NAME
       which - locate a command

SYNOPSIS
       which [-a] filename ...

DESCRIPTION
       which  returns  the  pathnames of the files (or links) which would be executed in the current environment, had its arguments been given as commands in a strictly POSIX-conformant shell.  It does this by searching the PATH for executable files matching
       the names of the arguments. It does not follow symbolic links.

OPTIONS
       -a     print all matching pathnames of each argument

EXIT STATUS
       0      if all specified commands are found and executable

       1      if one or more specified commands is nonexistent or not executable

       2      if an invalid option is specified

Debian                                                                                                                      1 May 2009                                                                                                                    WHICH(1)

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stgeke commented Feb 13, 2017

@RonRahaman Yes please send me your fix

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@stgeke, I sent you the fixes to NekTests.py in this PR:
https://github.com/stgeke/Nek5000/pull/2

Changed default location of makenek in NekTests.py
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Looks like only the eddy and kov_st_state tests fail now. They fail with this error:

 call userchk

        0  0.0000E+00 Write checkpoint:
       0       0 OPEN: eddy_uv0.f00001
byte_write() :: fopen failure!
byte_write() :: fopen failure!
ERROR: Error writing header in mfo_write_hdr.   ierr=  1 
  
call exitt: dying ...

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2 participants