Trilinos issueshttps://gitlab.osti.gov/jmwille/Trilinos/-/issues2019-03-07T21:39:34Zhttps://gitlab.osti.gov/jmwille/Trilinos/-/issues/4553SEACAS Building issues, holding up Trilinos2019-03-07T21:39:34ZJames WillenbringSEACAS Building issues, holding up Trilinos*Created by: Tdub1229*
[ 22%] Building C object packages/seacas/scripts/CMakeFiles/getopt.seacas.dir/getopt.seacas.c.o
Undefined symbols for architecture x86_64:
"_H5get_libversion", referenced from:
_ex_print_config in libex...*Created by: Tdub1229*
[ 22%] Building C object packages/seacas/scripts/CMakeFiles/getopt.seacas.dir/getopt.seacas.c.o
Undefined symbols for architecture x86_64:
"_H5get_libversion", referenced from:
_ex_print_config in libexodus.a(ex_utils.c.o)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [packages/seacas/applications/exo_format/exo_format] Error 1
make[1]: *** [packages/seacas/applications/exo_format/CMakeFiles/exo_format.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 22%] Linking C executable getopt.seacas
[ 22%] Built target getopt.seacas
make: *** [all] Error 2
-->
I recently updated my Mac and operating systems (10.14) however, this has caused some difficulty trying to reinstall trilinos Packages. I get this error, and I am not sure if there are any solutions or if there is a way in which I can bypass this.
I can post my cmake and installation logs if needed.
Thanks
https://gitlab.osti.gov/jmwille/Trilinos/-/issues/3891Link failure for test SEACASIoss_Utst_structured_decomp.exe in Trilinos-atdm-...2018-12-07T20:11:49ZJames WillenbringLink failure for test SEACASIoss_Utst_structured_decomp.exe in Trilinos-atdm-cee-rhel6-intel-opt-serial starting 11/3/2018*Created by: bartlettroscoe*
CC: @trilinos/seacas , @kddevin (Trilinos <product-area-name> Product Lead), @bartlettroscoe, @fryeguy52
## Next Action Status
Decide what to do with this failing test.
## Description
As shown in...*Created by: bartlettroscoe*
CC: @trilinos/seacas , @kddevin (Trilinos <product-area-name> Product Lead), @bartlettroscoe, @fryeguy52
## Next Action Status
Decide what to do with this failing test.
## Description
As shown in [this query](https://testing.sandia.gov/cdash-dev-view/index.php?project=Trilinos&date=2018-11-16&filtercount=2&showfilters=1&filtercombine=and&field1=buildname&compare1=65&value1=Trilinos-atdm-cee-rhel6-intel&field2=buildstarttime&compare2=84&value2=now) the executable `SEACASIoss_Utst_structured_decomp.exe` started to fail to link in the build `Trilinos-atdm-cee-rhel6-intel` starting on 11/3/2018. This in turn cased the test defined using this executable `SEACASIoss_Utst_structured_decomp_MPI_1 ` to be not run.
The link failure is shown [here](https://testing.sandia.gov/cdash-dev-view/viewBuildError.php?buildid=4133432) which shows:
```
/projects/sparc/tpls/cee-rhel6-new/cgns-develop/cee-cpu_intel-17.0.1_intelmpi-5.1.2/lib/libcgns.a(ADFH.c.o): In function `children_ids':
ADFH.c:(.text+0x18b): undefined reference to `H5Gopen2'
ADFH.c:(.text+0x1c3): undefined reference to `H5Gclose'
/projects/sparc/tpls/cee-rhel6-new/cgns-develop/cee-cpu_intel-17.0.1_intelmpi-5.1.2/lib/libcgns.a(ADFH.c.o): In function `compare_children':
ADFH.c:(.text+0x1f4): undefined reference to `H5Gget_objinfo'
/projects/sparc/tpls/cee-rhel6-new/cgns-develop/cee-cpu_intel-17.0.1_intelmpi-5.1.2/lib/libcgns.a(ADFH.c.o): In function `get_str_att':
ADFH.c:(.text+0x26c): undefined reference to `H5Aopen_name'
ADFH.c:(.text+0x28c): undefined reference to `H5Aiterate2'
ADFH.c:(.text+0x2e8): undefined reference to `H5Aget_type'
ADFH.c:(.text+0x301): undefined reference to `H5Aread'
ADFH.c:(.text+0x30b): undefined reference to `H5Tclose'
ADFH.c:(.text+0x312): undefined reference to `H5Aclose'
ADFH.c:(.text+0x4b7): undefined reference to `H5Aclose'
...
```
The new commits that were pulled the day that these failures started are show, for example, [here](https://testing.sandia.gov/cdash-dev-view/viewNotes.php?buildid=4133432#!#note6). Looking over those commits there does not seem to be any that could impact either that ATDM Trilinos configuration or the SEACAS package itself. And there does not seem to have been an env change in the HDF5 libs that could have triggered this link failure (more on that in a later comment).
## Current Status on CDash
As shown in [this query](https://testing.sandia.gov/cdash-dev-view/index.php?project=Trilinos&date=2018-11-16&filtercount=2&showfilters=1&filtercombine=and&field1=buildname&compare1=65&value1=Trilinos-atdm-cee-rhel6-intel&field2=buildstarttime&compare2=84&value2=now), the build `Trilinos-atdm-cee-rhel6-intel` was (prematurely) disabled on 11/11/2018 and therefore this failure can not be seen on the current CDash site (but I did reproduce this failure locally while working on #3871 so this build error still exists).
## Steps to Reproduce
One should be able to reproduce this failure on any CEE RHEL6 machine using the 'cee-rhel6' env as described in:
* https://github.com/trilinos/Trilinos/blob/develop/cmake/std/atdm/README.md
More specifically, the commands given for the s 'cee-rhel6' env are provided at:
* https://github.com/trilinos/Trilinos/blob/develop/cmake/std/atdm/README.md#cee-rhel6
The exact commands to reproduce this build error should be:
```
$ cd <some_build_dir>/
$ source $TRILINOS_DIR/cmake/std/atdm/load-env.sh cee-rhel6-intel-opt-serial
$ cmake \
-GNinja \
-DTrilinos_CONFIGURE_OPTIONS_FILE:STRING=cmake/std/atdm/ATDMDevEnv.cmake \
-DTrilinos_ENABLE_TESTS=ON -DTrilinos_ENABLE_SEACAS=ON \
-DSEACASIoss_Utst_structured_decomp_EXE_DISABLE=OFF \
-DSEACASIoss_Utst_structured_decomp_DISABLE=OFF \
$TRILINOS_DIR
$ make NP=16
```
Initial cleanup of new ATDM builds of Trilinoshttps://gitlab.osti.gov/jmwille/Trilinos/-/issues/3496SEACAS tests 'Not Run' on ATDM mutrino builds2018-11-30T11:15:41ZJames WillenbringSEACAS tests 'Not Run' on ATDM mutrino builds*Created by: fryeguy52*
CC: @trilinos/seacas , @kddevin (Trilinos Data Services Product Lead), @bartlettroscoe
## Next Action Status
Tests disabled in PR in #3530 merged on 9/29/2018 and these tests went missing in this build o...*Created by: fryeguy52*
CC: @trilinos/seacas , @kddevin (Trilinos Data Services Product Lead), @bartlettroscoe
## Next Action Status
Tests disabled in PR in #3530 merged on 9/29/2018 and these tests went missing in this build on 9/30/2018 as shown [here](https://testing.sandia.gov/cdash-dev-view/viewTest.php?buildid=3993235). Next: Fix the tests?
## Description
several seacas tests are showing up as "not run" in the ATDM builds on mutrino. As shown [here](https://testing.sandia.gov/cdash-dev-view/queryTests.php?project=Trilinos&date=2018-09-24&filtercount=4&showfilters=1&filtercombine=and&field1=groupname&compare1=61&value1=ATDM&field2=site&compare2=61&value2=mutrino&field3=status&compare3=62&value3=passed&field4=buildstarttime&compare4=83&value4=2018-09-01) the tests are:
* SEACASAprepro_aprepro_test_exodus
* SEACASIoss_exodus32_to_exodus32
* SEACASIoss_exodus32_to_exodus32_pnetcdf
* SEACASIoss_exodus32_to_exodus64
are not run in the build:
* Trilinos-atdm-mutrino-intel-opt-openmp-HSW
the test output on CDash for all 4 of these is:
```
Unable to find required file: CMND_PATH-NOTFOUND
```
## Steps to Reproduce
One should be able to reproduce this failure on the machine mutrino as described in:
* https://github.com/trilinos/Trilinos/blob/develop/cmake/std/atdm/README.md
More specifically, the commands given for the system mutrino are provided at:
* https://github.com/trilinos/Trilinos/blob/develop/cmake/std/atdm/README.md#mutrino
The exact commands to reproduce this issue should be:
```
$ cd <some_build_dir>/
$ source $TRILINOS_DIR/cmake/std/atdm/load-env.sh intel-opt-openmp-HSW
$ cmake \
-DTrilinos_CONFIGURE_OPTIONS_FILE:STRING=cmake/std/atdm/ATDMDevEnv.cmake \
-DTrilinos_ENABLE_TESTS=ON -DTrilinos_ENABLE_SEACAS=ON \
$TRILINOS_DIR
$ make -j16
$ salloc -N 1 -p standard -J $JOB_NAME ctest -j16
```
Keep promoted "ATDM" builds of Trilinos cleanhttps://gitlab.osti.gov/jmwille/Trilinos/-/issues/1751Discuss and document workflow for directly snapshotting SEACAS into Trilinos ...2018-06-26T12:49:47ZJames WillenbringDiscuss and document workflow for directly snapshotting SEACAS into Trilinos to better serve ATDM*Created by: bartlettroscoe*
**Next Action Status:**
@gdsjaar to implement agreed to workflow on SEACAS github site then start doing new workflow ...
**CC:** @trilinos/framework, @gsjaardema
**Description:**
This story is t...*Created by: bartlettroscoe*
**Next Action Status:**
@gdsjaar to implement agreed to workflow on SEACAS github site then start doing new workflow ...
**CC:** @trilinos/framework, @gsjaardema
**Description:**
This story is to document a discussion and the final workflow for allowing @gsjaardema to directly SEACAS directly into Trilinos/packages/seacas/ in addition to shapshotting SEACAS into Sierra.base/seacas/ and then having that snapshotted from ther into Trilinos/packages/seacas/. The nature of the snapshotting process (i.e. never a merge) eliminates the potential for merge conflicts that might make the snapshotting from Sierra.base/seacas/ to Trilinos/packages/seacas/ more difficult. And this would allow @gsjaardema control to address issues for ATDM customers very quickly and simplify the version control and configuration of Trilinos for ATDM customers. For more background and discussion, see:
* https://software-srn.sandia.gov/jira/browse/SPAR-277