Skip to content

Wrf pkg intel and pgi#3

Merged
baberlevi merged 2 commits intoResearchIT:packages/wrffrom
exactlab:wrf_pkg_intel_and_pgi
Jan 8, 2019
Merged

Wrf pkg intel and pgi#3
baberlevi merged 2 commits intoResearchIT:packages/wrffrom
exactlab:wrf_pkg_intel_and_pgi

Conversation

@bebosudo
Copy link
Copy Markdown

@bebosudo bebosudo commented Dec 18, 2018

Add more compiler choices.
Prepend pgi path since pgf90 wasn't found.
Use a tempfile to write the input file to the configure.
Enable the parallel build.

Unfortunately the build with PGI+gfortran fails with:

ar ru ../main/libwrflib.a module_driver_constants.o module_domain_type.o module_streams.o module_domain.o  module_integrate.o module_timing.o module_configure.o module_tiles.o module_machine.o module_nesting.o module_wrf_error.o module_state_description.o module_sm.o module_io.o module_comm_dm.o module_comm_dm_0.o module_comm_dm_1.o module_comm_dm_2.o module_comm_dm_3.o module_comm_dm_4.o module_comm_nesting_dm.o module_dm.o module_quilt_outbuf_ops.o module_io_quilt.o module_intermediate_nmm.o module_cpl.o module_cpl_oasis3.o module_clear_halos.o wrf_num_bytes_between.o wrf_shutdown.o wrf_debug.o libmassv.o collect_on_comm.o hires_timer.o clog.o nl_get_0_routines.o nl_get_1_routines.o nl_get_2_routines.o nl_get_3_routines.o nl_get_4_routines.o nl_get_5_routines.o nl_get_6_routines.o nl_get_7_routines.o nl_set_0_routines.o nl_set_1_routines.o nl_set_2_routines.o nl_set_3_routines.o nl_set_4_routines.o nl_set_5_routines.o nl_set_6_routines.o nl_set_7_routines.o  module_alloc_space_0.o module_alloc_space_1.o module_alloc_space_2.o module_alloc_space_3.o module_alloc_space_4.o module_alloc_space_5.o module_alloc_space_6.o module_alloc_space_7.o module_alloc_space_8.o module_alloc_space_9.o
ar: creating ../main/libwrflib.a
ar: module_integrate.o: No such file or directory
make[2]: [framework] Error 1 (ignored)
ranlib ../main/libwrflib.a
ranlib: '../main/libwrflib.a': No such file
make[2]: [framework] Error 1 (ignored)
make[2]: Leaving directory `/dev/shm/spack/stage/root/spack-stage/spack-stage-JexrAm/WRF/frame'
make[2]: Entering directory `/dev/shm/spack/stage/root/spack-stage/spack-stage-JexrAm/WRF/external/io_netcdf'
x=`echo "f77" | awk '{print $1}'` ; export x ; \
if [ $x = "gfortran" ] ; then \
           echo removing external declaration of iargc for gfortran ; \
   /lib/cpp -P -nostdinc -P -traditional-cpp -DUSE_NETCDF4_FEATURES -DWRFIO_NCD_LARGE_FILE_SUPPORT -I/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\
        else \
   /lib/cpp -P -nostdinc -P -traditional-cpp -DUSE_NETCDF4_FEATURES -DWRFIO_NCD_LARGE_FILE_SUPPORT -I/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \
        fi
diffwrf.F90:55:0: fatal error: netcdf.inc: No such file or directory
 #include "netcdf.inc"
 ^

Any idea? Should I prepend to CPATH also the include dir of netcdf-fortran?

@baberlevi baberlevi merged commit 1432c09 into ResearchIT:packages/wrf Jan 8, 2019
@bebosudo bebosudo deleted the wrf_pkg_intel_and_pgi branch January 9, 2019 12:11
baberlevi pushed a commit that referenced this pull request Jul 25, 2019
Bug relates to the interplay between:
1. random dict orders in python 3.5
2. bugfix in initial implementation of stacks for `_concretize_dependencies`
   when `self._dependencies` is empty
3. bug in coconcretization algorithm computation of split specs

Result was transient hang in coconcretization.
Fixed #3 (bug in coconcretization) to resolve.
codeandkey pushed a commit that referenced this pull request Apr 7, 2020
* Fixed building coreutils on Darwin

* Bump nano version to 4.9

* Coreutils: Add program prefix g so we don't conflict with Apple utilities

* Fix intendation

* Make format more spack like

* Removed unnecesary changes

* Merge branch 'develop' of github.com:DiegoMagdaleno/spack into develop

Fix linking libgit2 on Darwin

* Revert "Merge pull request #3 from spack/develop"

This reverts commit 58dbbdb, reversing
changes made to dd7a413.

* Revert "Revert "Merge pull request #3 from spack/develop""

This reverts commit f956aa7.

* Revert "Merge branch 'develop' of github.com:DiegoMagdaleno/spack into develop"

This reverts commit 50321f7.
codeandkey pushed a commit that referenced this pull request Jun 17, 2020
Whenever attempting to use any ncurses functionality within cscope, a
page fault would result within the ncurses library.

    Program received signal SIGSEGV, Segmentation fault.
    0x00007ffff7fad3cf in termattrs_sp () from .../lib/libncursesw.so.6
    (gdb) bt
    #0  0x00007ffff7fad3cf in termattrs_sp () from .../lib/libncursesw.so.6
    #1  0x00007ffff7faa794 in _nc_setupscreen_sp () from .../lib/libncursesw.so.6
    #2  0x00007ffff7fa614c in newterm_sp () from .../lib/libncursesw.so.6
    #3  0x00007ffff7fa65b9 in newterm () from .../lib/libncursesw.so.6
    #4  0x00007ffff7fa2970 in initscr () from .../lib/libncursesw.so.6
    #5  0x0000000000403dc2 in main (argc=<optimized out>, argv=0x7fffffffcea8) at main.c:574

This is due to a conflict between libtinfo.so and libtinfow.so. Both are
linked into cscope:

    $ ldd $(which cscope)
    /bin/bash: .../lib/libtinfo.so.6: no version information available (required by /bin/bash)
        linux-vdso.so.1 (0x00007fff5dbcb000)
        libncursesw.so.6 => .../lib/libncursesw.so.6 (0x00007f435cc69000)
        libtinfo.so.6 => .../lib/libtinfo.so.6 (0x00007f435cc2c000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f435ca29000)
        libtinfow.so.6 => .../lib/libtinfow.so.6 (0x00007f435c9e8000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f435cca7000)

Specifically linking libtinfow.so instead of libtinfo.so resolves the
issue.

All instances of '...' above represent the path to the installed ncurses
for Spack.
baberlevi pushed a commit that referenced this pull request Aug 17, 2020
* Add Collier and SysCalc recipes

* Remove extra syscalc version

* Build collier with -j1 for @:1.2.4

* Add recipe for gosam-contrib

* Update gosam-contrib recipe with 'provides'

* Madgraph recipe, first version

* Finalize madgraph recipe + flake8

* Make py2 version of madgraph default; fix hash for syscalc; fix patch

* Handle virtual packages (#3)

* Update package.py

* Update packages.yaml

* Remove virtual packages - pt. 1

* Remove virtual packages - pt. 2

* Changes from review - pt. 1

* Changes from code review - pt. 2

* Update var/spack/repos/builtin/packages/collier/package.py

Co-authored-by: Adam J. Stewart <[email protected]>

* Update var/spack/repos/builtin/packages/madgraph5amc/package.py

Co-authored-by: Adam J. Stewart <[email protected]>

* Add hash for version 2.7.2 (available in our private mirror)

* Fixes for 2.7.3 family

* Patches for 2.7.3{.py3,}{.atlas,}

* Fix hash of syscalc

* Hack to fix concretization (2.7.3 matches 2.7.3.py3)

* Add conflict statement (reported to devs)

* Apply suggestions from code review

Co-authored-by: Adam J. Stewart <[email protected]>

* Update package.py

* Delete madgraph5amc-2.7.2.atlas.patch

* Delete madgraph5amc-2.7.2.patch

* Update package.py

* Apply suggestions from code review

Co-authored-by: Adam J. Stewart <[email protected]>

Co-authored-by: iarspider <[email protected]>
Co-authored-by: Adam J. Stewart <[email protected]>
snehring pushed a commit that referenced this pull request Aug 9, 2021
* Set LIBVER and LIBMAJOR

* Typo fix

* Fix 2

* Fix #3
snehring pushed a commit that referenced this pull request Apr 26, 2023
1. support version 3.1.3, which now depends on sundials@6

2. support version 3.1.2:, which broke the two patch files and
   therefore the two patch files have been replaced by more flexible
   filter_file() commands inside a patch() function.

3. rename the variant for python extension from using the package name
   "+pyuqtk" to the more standard "+python"

4. add maintainers @omsai and the upstream developer @bjdebus who
   offered to help with the spack packaging.

5. swig should only be a build-time dependency.  swig is only
   necessary until @:3.1.0

6. confirmed python dependencies are correct by inspecting imports,
   subset python dependencies type to build, run, and confirmed all
   31 build-time tests pass including the 9 python tests:

```console
$ spack env create uqtk-dev
$ spack add [email protected]
$ spack install --test root && cat $(spack location -i uqtk)/.spack/install-time-test-log.txt
==> Testing package uqtk-3.1.3-nok6fut
==> [2023-04-19-14:56:25.005361] Running build-time tests
==> [2023-04-19-14:56:25.005536] RUN-TESTS: build-time tests [check]
==> [2023-04-19-14:56:25.009543] '/home/omsai/src/spack/opt/spack/linux-pureos10-skylake/gcc-10.2.1/gmake-4.4.1-b6g4apmfvxz3bn4eabh37dehcrg65fj7/bin/make' '-j4' '-n' 'test'
==> [2023-04-19-14:56:25.014903] '/home/omsai/src/spack/opt/spack/linux-pureos10-skylake/gcc-10.2.1/gmake-4.4.1-b6g4apmfvxz3bn4eabh37dehcrg65fj7/bin/make' '-j4' 'test'
Running tests...
/home/omsai/src/spack/opt/spack/linux-pureos10-skylake/gcc-10.2.1/cmake-3.26.3-zjmsfz23j5l4ytniz26uzvxonlu5qebr/bin/ctest --force-new-ctest-process
Test project /tmp/omsai/spack-stage/spack-stage-uqtk-3.1.3-nok6fut47h42cnaau7wkoohgqy5f2qqa/spack-build-nok6fut
      Start  1: ArrayReadAndWrite
      Start  2: ArrayDelColumn
      Start  3: Array1DMiscTest
      Start  4: Array2DMiscTest
 1/31 Test  #1: ArrayReadAndWrite ................   Passed    0.01 sec
      Start  5: ArraySortTest
 2/31 Test  #2: ArrayDelColumn ...................   Passed    0.01 sec
      Start  6: MultiIndexTest
 3/31 Test  #3: Array1DMiscTest ..................   Passed    0.01 sec
      Start  7: CorrTest
 4/31 Test  #4: Array2DMiscTest ..................   Passed    0.01 sec
      Start  8: QuadLUTest
 5/31 Test  #5: ArraySortTest ....................   Passed    0.02 sec
      Start  9: MCMC2dTest
 6/31 Test  #6: MultiIndexTest ...................   Passed    0.01 sec
      Start 10: MCMCRandomTest
 7/31 Test  #8: QuadLUTest .......................   Passed    0.02 sec
      Start 11: MCMCNestedTest
 8/31 Test #10: MCMCRandomTest ...................   Passed    0.02 sec
      Start 12: Deriv1dTest
 9/31 Test #12: Deriv1dTest ......................   Passed    0.01 sec
      Start 13: SecondDeriv1dTest
10/31 Test #13: SecondDeriv1dTest ................   Passed    0.01 sec
      Start 14: GradHessianTest
11/31 Test #11: MCMCNestedTest ...................   Passed    0.03 sec
      Start 15: GradientPCETest
12/31 Test #14: GradHessianTest ..................   Passed    0.01 sec
      Start 16: PCE1dTest
13/31 Test #15: GradientPCETest ..................   Passed    0.01 sec
      Start 17: PCEImplTest
14/31 Test #16: PCE1dTest ........................   Passed    0.01 sec
      Start 18: PCELogTest
15/31 Test #18: PCELogTest .......................   Passed    0.01 sec
      Start 19: Hessian2dTest
16/31 Test #19: Hessian2dTest ....................   Passed    0.01 sec
      Start 20: BCS1dTest
17/31 Test #20: BCS1dTest ........................   Passed    0.01 sec
      Start 21: BCS2dTest
18/31 Test #21: BCS2dTest ........................   Passed    0.01 sec
      Start 22: LowRankRegrTest
19/31 Test #22: LowRankRegrTest ..................   Passed    0.01 sec
      Start 23: PyModTest
20/31 Test #17: PCEImplTest ......................   Passed    0.07 sec
      Start 24: PyArrayTest
21/31 Test #23: PyModTest ........................   Passed    0.08 sec
      Start 25: PyArrayTest2
22/31 Test #25: PyArrayTest2 .....................   Passed    0.30 sec
      Start 26: PyQuadTest
23/31 Test #24: PyArrayTest ......................   Passed    1.44 sec
      Start 27: PyBCSTest1D
24/31 Test #26: PyQuadTest .......................   Passed    1.68 sec
      Start 28: PyBCSTest2D
25/31 Test #27: PyBCSTest1D ......................   Passed    1.66 sec
      Start 29: PyBADPTest
26/31 Test  #7: CorrTest .........................   Passed    3.43 sec
      Start 30: PyRegressionTest
27/31 Test #28: PyBCSTest2D ......................   Passed    1.50 sec
      Start 31: PyGalerkinTest
28/31 Test  #9: MCMC2dTest .......................   Passed    3.90 sec
29/31 Test #29: PyBADPTest .......................   Passed    1.66 sec
30/31 Test #30: PyRegressionTest .................   Passed    1.72 sec
31/31 Test #31: PyGalerkinTest ...................   Passed    1.63 sec

100% tests passed, 0 tests failed out of 31

Total Test time (real) =   5.35 sec
==> [2023-04-19-14:56:30.382797] '/home/omsai/src/spack/opt/spack/linux-pureos10-skylake/gcc-10.2.1/gmake-4.4.1-b6g4apmfvxz3bn4eabh37dehcrg65fj7/bin/make' '-j4' '-n' 'check'
==> [2023-04-19-14:56:30.385983] Target 'check' not found in Makefile
```
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants