Trilinos issueshttps://gitlab.osti.gov/jmwille/Trilinos/-/issues2020-07-22T01:04:26Zhttps://gitlab.osti.gov/jmwille/Trilinos/-/issues/4973Trilinos seacas build issue on mayer with ARM compiler2020-07-22T01:04:26ZJames WillenbringTrilinos seacas build issue on mayer with ARM compiler*Created by: ikalash*
I'm encountering a build error when trying to build Trilinos develop on mayer with the ARM compiler (module load devpack-arm/20190201). Here is the error:
```
[ 41%] Building CXX object packages/seacas/libraries...*Created by: ikalash*
I'm encountering a build error when trying to build Trilinos develop on mayer with the ARM compiler (module load devpack-arm/20190201). Here is the error:
```
[ 41%] Building CXX object packages/seacas/libraries/ioss/src/CMakeFiles/Ioss.dir/Ioss_Node.C.o
[ 41%] Linking CXX executable nem_slice
Scanning dependencies of target mapvar
[ 41%] Building Fortran object packages/seacas/applications/mapvar/CMakeFiles/mapvar.dir/getbnd.f.o
[ 41%] Building Fortran object packages/seacas/applications/mapvar/CMakeFiles/mapvar.dir/mapvar.f.o
F90-S-0029-Illegal hexadecimal constant: Seehttps://github.com/gsjaardema/seacas/packages (/mscratch/albany/mayer/nightlyCDashTrilinos/repos/Trilinos/packages/seacas/applications/mapvar/mapvar.f: 417)
F90-S-0034-Syntax error at or near non-decimal constant 0 (/mscratch/albany/mayer/nightlyCDashTrilinos/repos/Trilinos/packages/seacas/applications/mapvar/mapvar.f: 417)
F90-S-0029-Illegal hexadecimal constant: Seehttps://github.com/gsjaardema/seacas/packages (/mscratch/albany/mayer/nightlyCDashTrilinos/repos/Trilinos/packages/seacas/applications/mapvar/mapvar.f: 428)
F90-S-0034-Syntax error at or near non-decimal constant 0 (/mscratch/albany/mayer/nightlyCDashTrilinos/repos/Trilinos/packages/seacas/applications/mapvar/mapvar.f: 428)
0 inform, 0 warnings, 4 severes, 0 fatal for mapvar
[ 41%] Building Fortran object packages/seacas/applications/mapvar/CMakeFiles/mapvar.dir/mklstv.f.o
[ 41%] Built target nem_slice
[ 41%] Building Fortran object packages/seacas/applications/mapvar/CMakeFiles/mapvar.dir/mkrnk.f.o
[ 41%] Building Fortran object packages/seacas/applications/mapvar/CMakeFiles/mapvar.dir/rank.f.o
[ 41%] Building Fortran object packages/seacas/applications/mapvar/CMakeFiles/mapvar.dir/srchge.f.o
[ 41%] Building Fortran object packages/seacas/applications/mapvar/CMakeFiles/mapvar.dir/srchgt.f.o
Scanning dependencies of target mapvar-kd
[ 41%] Building Fortran object packages/seacas/applications/mapvar-kd/CMakeFiles/mapvar-kd.dir/mapvar-kd.f.o
F90-S-0029-Illegal hexadecimal constant: Seehttps://github.com/gsjaardema/seacas/packages (/mscratch/albany/mayer/nightlyCDashTrilinos/repos/Trilinos/packages/seacas/applications/mapvar-kd/mapvar-kd.f: 285)
F90-S-0034-Syntax error at or near non-decimal constant 0 (/mscratch/albany/mayer/nightlyCDashTrilinos/repos/Trilinos/packages/seacas/applications/mapvar-kd/mapvar-kd.f: 285)
```
According to my colleague @jewatkins, the build worked just fine on April 9. Our configure script is attached.
[do-cmake-trilinos-arm-serial.txt](https://github.com/trilinos/Trilinos/files/3099602/do-cmake-trilinos-arm-serial.txt)
@trilinos/seacas
https://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/4514SEACAS: Remove Build Warnings2019-05-01T18:29:55ZJames WillenbringSEACAS: Remove Build Warnings*Created by: ZUUL42*
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<!---
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@trilinos/seacas
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## Expectations
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SEACAS builds should not emit any warnings that will be promoted to errors once Werror is set in the GCC 7.2.0 automated build.
## Current Behavior
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-->
Currently SEACAS has a number of warnings that need to be handled before we can set Werror for all packages.
A recent test build was performed with -Werror set for SEACAS. The CDash report can be found [here](https://testing-vm.sandia.gov/cdash/viewBuildError.php?buildid=4624441).
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Issue #3178 is working toward turning Warnings as Errors on for all packages.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/3663Compilation error due to seacas on some platforms2018-11-06T16:22:01ZJames WillenbringCompilation error due to seacas on some platforms*Created by: ikalash*
Trilinos failed to compile in last night's Albany tests on the NERSC machines (Cori, Edison) and some machines at SNL (@lxmota 's Fedora 28 machine, algol) due to what appears to be a seacas issue:
```
repos/Tril...*Created by: ikalash*
Trilinos failed to compile in last night's Albany tests on the NERSC machines (Cori, Edison) and some machines at SNL (@lxmota 's Fedora 28 machine, algol) due to what appears to be a seacas issue:
```
repos/Trilinos/packages/seacas/libraries/exodus/src/ex_utils.c:1664:17: error: 'exoid' undeclared (first use in this function); did you mean 'exit'?
```
The full output can be found here: https://my.cdash.org/viewBuildError.php?buildid=1545426 or here: http://cdash.sandia.gov/CDash-2-3-0/viewBuildError.php?buildid=77215 . Curiously enough the problem didn't occur in the other Albany nightly tests, so it may be machine/compiler-specific or due to the specific NERSC configuration.
@trilinos/seacas https://gitlab.osti.gov/jmwille/Trilinos/-/issues/3652Seacas ParaviewCatalystIossAdapter CMakeLists file has the wrong comment type2019-01-02T17:46:36ZJames WillenbringSeacas ParaviewCatalystIossAdapter CMakeLists file has the wrong comment type*Created by: jrood-nrel*
https://github.com/trilinos/Trilinos/blob/develop/packages/seacas/libraries/ioss/src/visualization/ParaViewCatalystIossAdapter/parser/CMakeLists.txt has the wrong type of comments for CMake in it so it causes er...*Created by: jrood-nrel*
https://github.com/trilinos/Trilinos/blob/develop/packages/seacas/libraries/ioss/src/visualization/ParaViewCatalystIossAdapter/parser/CMakeLists.txt has the wrong type of comments for CMake in it so it causes errors when trying to configure it.https://gitlab.osti.gov/jmwille/Trilinos/-/issues/3631SEACASIoss CGNS tests failing in ATDM configuration in cee-rhel6-intel-opt-se...2018-11-30T03:05:04ZJames WillenbringSEACASIoss CGNS tests failing in ATDM configuration in cee-rhel6-intel-opt-serial builds*Created by: fryeguy52*
CC: @trilinos/seacas , @kddevin (Trilinos Data Services Product Lead), @bartlettroscoe
## Next Action Status
The Intel install of the CGNS tools was fixed on 10/19/2018 and these SEACAS CGNS tests pass o...*Created by: fryeguy52*
CC: @trilinos/seacas , @kddevin (Trilinos Data Services Product Lead), @bartlettroscoe
## Next Action Status
The Intel install of the CGNS tools was fixed on 10/19/2018 and these SEACAS CGNS tests pass on 10/20/2018 as shown [here](https://testing.sandia.gov/cdash-dev-view/viewTest.php?onlydelta&buildid=4073426).
## Description
As shown in [this query](https://testing.sandia.gov/cdash-dev-view/queryTests.php?project=Trilinos&date=2018-10-15&filtercount=2&showfilters=1&filtercombine=and&field1=buildname&compare1=65&value1=Trilinos-atdm-cee-rhel6-&field2=status&compare2=62&value2=passed) the tests:
* SEACASIoss_structured_cgns_roundtrip_zgc
* SEACASIoss_structured_cgns_roundtrip_single_fpp_single_fields
* SEACASIoss_structured_cgns_roundtrip_fpp2
* SEACASIoss_structured_cgns_roundtrip_fpp
* SEACASIoss_structured_cgns_roundtrip_fields
* SEACASIoss_structured_cgns_roundtrip_bump
* SEACASIoss_structured_cgns_roundtrip
* SEACASIoss_generated64_to_unstructured_cgns
* SEACASIoss_generated32_to_unstructured_cgns
* SEACASIoss_exodus64_to_unstructured_cgns
* SEACASIoss_exodus32_to_unstructured_cgns
are failing in the builds:
* Trilinos-atdm-cee-rhel6-intel-opt-serial
many of these are showing something like:
```
/projects/sparc/tpls/cee-rhel6-new/cgns-develop/cee-cpu_intel-17.0.1_intelmpi-5.1.2/bin/cgnslist: symbol lookup error: /sierra/sntools/SDK/compilers/intel/composer_xe_2017.1.132/compilers_and_libraries/linux/lib/intel64/libifport.so.5: undefined symbol: __FFfrand
```
## Steps to Reproduce
One should be able to reproduce this failure on any CEE LAN RHEL6 SRN as described in:
* https://github.com/trilinos/Trilinos/blob/develop/cmake/std/atdm/README.md
More specifically, the commands given for the systemCEE LAN RHEL6 SRN are provided at:
* https://github.com/trilinos/Trilinos/blob/develop/cmake/std/atdm/README.md#cee-rhel6-environment
The exact commands to reproduce this issue 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 \
$TRILINOS_DIR
$ make NP=16
$ ctest -j16
```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/3346SEACAS not included files...in neither src directory nor install directory2018-11-30T03:12:47ZJames WillenbringSEACAS not included files...in neither src directory nor install directory*Created by: kyungjoo-kim*
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@trilinos/seacas...*Created by: kyungjoo-kim*
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@trilinos/seacas
After I installed Trilinos with SEACAS and compile a code against them, I have cmake error reporting following packages are missing.
```
CMake Error at /home/kyukim/Work/lib/trilinos/install/white/empire/release-k80-cuda-9.2/lib/cmake/SEACAS/SEACASConfig.cmake:146 (INCLUDE):
INCLUDE could not find load file:
/home/kyukim/Work/lib/trilinos/install/white/empire/release-k80-cuda-9.2/lib/cmake/SEACAS/../SEACASTxtexo/SEACASTxtexoConfig.cmake
/home/kyukim/Work/lib/trilinos/install/white/empire/release-k80-cuda-9.2/lib/cmake/SEACAS/../SEACASNumbers/SEACASNumbersConfig.cmake
/home/kyukim/Work/lib/trilinos/install/white/empire/release-k80-cuda-9.2/lib/cmake/SEACAS/../SEACASMapvar-kd/SEACASMapvar-kdConfig.cmake
/home/kyukim/Work/lib/trilinos/install/white/empire/release-k80-cuda-9.2/lib/cmake/SEACAS/../SEACASMapvar/SEACASMapvarConfig.cmake
/home/kyukim/Work/lib/trilinos/install/white/empire/release-k80-cuda-9.2/lib/cmake/SEACAS/../SEACASMapvarlib/SEACASMapvarlibConfig.cmake
/home/kyukim/Work/lib/trilinos/install/white/empire/release-k80-cuda-9.2/lib/cmake/SEACAS/../SEACASExplore/SEACASExploreConfig.cmake
/home/kyukim/Work/lib/trilinos/install/white/empire/release-k80-cuda-9.2/lib/cmake/SEACAS/../SEACASGrepos/SEACASGreposConfig.cmake
/home/kyukim/Work/lib/trilinos/install/white/empire/release-k80-cuda-9.2/lib/cmake/SEACAS/../SEACASGenshell/SEACASGenshellConfig.cmake
/home/kyukim/Work/lib/trilinos/install/white/empire/release-k80-cuda-9.2/lib/cmake/SEACAS/../SEACASGen3D/SEACASGen3DConfig.cmake
/home/kyukim/Work/lib/trilinos/install/white/empire/release-k80-cuda-9.2/lib/cmake/SEACAS/../SEACASGjoin/SEACASGjoinConfig.cmake
/home/kyukim/Work/lib/trilinos/install/white/empire/release-k80-cuda-9.2/lib/cmake/SEACAS/../SEACASEx1ex2v2/SEACASEx1ex2v2Config.cmake
/home/kyukim/Work/lib/trilinos/install/white/empire/release-k80-cuda-9.2/lib/cmake/SEACAS/../SEACASExotxt/SEACASExotxtConfig.cmake
/home/kyukim/Work/lib/trilinos/install/white/empire/release-k80-cuda-9.2/lib/cmake/SEACAS/../SEACASAlgebra/SEACASAlgebraConfig.cmake
/home/kyukim/Work/lib/trilinos/install/white/empire/release-k80-cuda-9.2/lib/cmake/SEACAS/../SEACASSuplib/SEACASSuplibConfig.cmake
/home/kyukim/Work/lib/trilinos/install/white/empire/release-k80-cuda-9.2/lib/cmake/SEACAS/../SEACASSupes/SEACASSupesConfig.cmake
/home/kyukim/Work/lib/trilinos/install/white/empire/release-k80-cuda-9.2/lib/cmake/SEACAS/../SEACASExoIIv2for32/SEACASExoIIv2for32Config.cmake
/home/kyukim/Work/lib/trilinos/install/white/empire/release-k80-cuda-9.2/lib/cmake/SEACAS/../SEACASExodus_for/SEACASExodus_forConfig.cmake
```
CMakeCache output indicates SEACAS has dependency on those packages
```
SEACAS_FULL_ENABLED_DEP_PACKAGES:INTERNAL=SEACASTxtexo;SEACASNumbers;SEACASNemspread;SEACASNemslice;SEACASMapvar-kd;SEACASMapvar;SEACASMapvarlib;SEACASExplore;SEACASGrepos;SEACASGenshell;SEACASGen3D;SEACASGjoin;SEACASEx1ex2v2;SEACASExo_\
format;SEACASExotxt;SEACASExomatlab;SEACASExodiff;SEACASEpu;SEACASEjoin;SEACASConjoin;SEACASAprepro;SEACASAlgebra;SEACASSuplibCpp;SEACASSuplibC;SEACASSuplib;SEACASSupes;SEACASAprepro_lib;SEACASChaco;SEACASIoss;SEACASNemesis;SEACASExoIIv\
2for32;SEACASExodus_for;SEACASExodus;Pamgen;Zoltan;Kokkos;KokkosAlgorithms;KokkosContainers;KokkosCore
```
## Expectations
<!---
Tell us what you think should happen, how you think things should work, what
you would like to see in the documentation, etc.
-->
Trilinos cmake system should be compiled with other cmake system used by applications. The dependence on missing packages should be configured correctly.
## Current Behavior
<!---
Tell us how the current behavior fails to meet your expectations in some way.
-->
cmake looks up missing packages.
## Motivation and Context
<!---
How has this expectation failure affected you? What are you trying to
accomplish? Why do we need to address this? What does it have to do with
anything? Providing context helps us come up with a solution that is most
useful in the real world.
-->
This does not compile with other applications that rely on cmake e.g., empire.
## Definition of Done
Corrrect cmake dependence.
- check install directory ``${INSTALL_DIR}/lib/cmake/SEACASConfig.cmake``
- check if it does not include ``INCLUDE("${CMAKE_CURRENT_LIST_DIR}/../SEACASTxtexo/SEACASTxtexoConfig.cmake") `` as well as all other packages listed above.
- or check CMakeCache does not include dependency on the packages above.
## Steps to Reproduce
Configure Trilinos with SEACAS
```
cmake \
-D BUILD_SHARED_LIBS:BOOL=${SHARED_LIBS} \
-D CMAKE_BUILD_TYPE:STRING=${BUILD_TYPE} \
-D CMAKE_C_COMPILER:FILEPATH="mpicc" \
-D CMAKE_C_FLAGS:STRING="${EXTRA_C_FLAGS}" \
-D CMAKE_CXX_COMPILER:FILEPATH="mpicxx" \
-D CMAKE_CXX_FLAGS:STRING="${EXTRA_CXX_FLAGS}" \
-D CMAKE_Fortran_COMPILER:FILEPATH="mpif77" \
-D CMAKE_Fortran_FLAGS:STRING="${EXTRA_F77_FLAGS}" \
-D CMAKE_SKIP_RULE_DEPENDENCY:BOOL=ON \
-D CMAKE_INSTALL_PREFIX:PATH=${INSTALL_DIR} \
-D CMAKE_VERBOSE_MAKEFILE:BOOL=OFF \
-D Trilinos_CXX11_FLAGS:STRING="-std=c++11" \
-D Trilinos_ENABLE_INSTALL_CMAKE_CONFIG_FILES:BOOL=ON \
-D Trilinos_VERBOSE_CONFIGURE:BOOL=OFF \
-D Trilinos_ENABLE_DEBUG:BOOL=OFF \
-D Trilinos_ENABLE_EXAMPLES:BOOL=${EXAMPLE} \
-D Trilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON \
-D Trilinos_ENABLE_Fortran:BOOL=OFF \
-D Trilinos_ENABLE_STRONG_CXX_COMPILE_WARNINGS:BOOL=OFF \
-D Trilinos_ENABLE_STRONG_C_COMPILE_WARNINGS:BOOL=OFF \
-D Trilinos_ENABLE_SHADOW_WARNINGS:BOOL=OFF \
-D Trilinos_ENABLE_TESTS:BOOL=${TEST} \
-D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF \
-D Trilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=OFF \
-D Trilinos_ENABLE_OpenMP:BOOL=${USE_OPENMP} \
-D Trilinos_ENABLE_Amesos:BOOL=ON \
-D Trilinos_ENABLE_Amesos2:BOOL=ON \
-D Trilinos_ENABLE_Belos:BOOL=ON \
-D Trilinos_ENABLE_KokkosCore:BOOL=ON \
-D Trilinos_ENABLE_KokkosAlgorithms:BOOL=ON \
-D Trilinos_ENABLE_ML:BOOL=ON \
-D Trilinos_ENABLE_MueLu:BOOL=ON \
-D Trilinos_ENABLE_Panzer:BOOL=ON \
-D Trilinos_ENABLE_Pamgen:BOOL=ON \
-D Trilinos_ENABLE_SEACAS:BOOL=ON \
-D Trilinos_ENABLE_SEACASIoss:BOOL=ON \
-D Trilinos_ENABLE_SEACASEx2ex1v2:BOOL=OFF \
-D Trilinos_ENABLE_Shards:BOOL=ON \
-D Trilinos_ENABLE_STK:BOOL=ON \
-D Trilinos_ENABLE_STKMesh:BOOL=ON \
-D Trilinos_ENABLE_STKUtil:BOOL=ON \
-D Trilinos_ENABLE_STKTopology:BOOL=ON \
-D Trilinos_ENABLE_STKSearch:BOOL=OFF \
-D Trilinos_ENABLE_STKTransfer:BOOL=OFF \
-D Trilinos_ENABLE_STKDoc_tests:BOOL=OFF \
-D Trilinos_ENABLE_STKUnit_tests:BOOL=OFF \
-D Trilinos_ENABLE_STKUnit_test_utils:BOOL=OFF \
-D Trilinos_ENABLE_Stokhos:BOOL=OFF \
-D Trilinos_ENABLE_Stratimikos:BOOL=ON \
-D Trilinos_ENABLE_Teko:BOOL=ON \
-D Trilinos_ENABLE_Tempus:BOOL=ON \
-D Trilinos_ENABLE_Zoltan:BOOL=ON \
-D Trilinos_ENABLE_Zoltan2:BOOL=ON \
-D EpetraExt_ENABLE_HDF5:BOOL=OFF \
-D Kokkos_ENABLE_OpenMP:BOOL=${USE_OPENMP} \
-D Kokkos_ENABLE_Pthread:BOOL=${USE_PTHREADS} \
-D Kokkos_ENABLE_Cuda_UVM:BOOL=${USE_CUDA} \
-D Kokkos_ENABLE_Cuda_Lambda:BOOL=${USE_CUDA} \
-D Kokkos_ENABLE_Debug_Bounds_Check:BOOL=${BOUNDS_CHECK} \
-D MueLu_ENABLE_Experimental:BOOL=ON \
-D Panzer_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON \
-D Panzer_ENABLE_TESTS:BOOL=OFF \
-D Phalanx_KOKKOS_DEVICE_TYPE:STRING="${NODE_TYPE}" \
-D Phalanx_SHOW_DEPRECATED_WARNINGS:BOOL=OFF \
-D SEACASExodus_ENABLE_MPI:BOOL=ON \
-D TeuchosCore_ENABLE_yaml-cpp:BOOL=ON \
-D Xpetra_ENABLE_Experimental:BOOL=ON \
-D TPL_ENABLE_GLM:BOOL=OFF \
-D TPL_ENABLE_Matio:BOOL=OFF \
-D TPL_ENABLE_SuperLU:BOOL=OFF \
-D TPL_ENABLE_X11:BOOL=OFF \
-D TPL_ENABLE_MPI:BOOL=ON \
-D TPL_ENABLE_BLAS:BOOL=ON \
-D TPL_BLAS_LIBRARIES:FILEPATH="-lblas" \
-D TPL_ENABLE_Boost:BOOL=ON \
-D Boost_INCLUDE_DIRS:FILEPATH="${BOOST_ROOT}/include" \ \
-D Boost_LIBRARY_DIRS:FILEPATH="${BOOST_ROOT}/lib" \
-D TPL_ENABLE_BoostLib:BOOL=ON \
-D BoostLib_INCLUDE_DIRS:FILEPATH="${BOOST_ROOT}/include" \
-D BoostLib_LIBRARY_DIRS:FILEPATH="${BOOST_ROOT}/lib" \
-D TPL_ENABLE_CUDA:BOOL=${USE_CUDA} \
-D TPL_ENABLE_CUSPARSE:BOOL=${USE_CUDA} \
-D TPL_ENABLE_LAPACK:BOOL=ON \
-D TPL_LAPACK_LIBRARIES:FILEPATH="-llapack" \
-D TPL_ENABLE_HDF5:BOOL=ON \
-D HDF5_INCLUDE_DIRS:FILEPATH="${HDF5_ROOT}/include" \
-D HDF5_LIBRARY_DIRS:FILEPATH="${HDF5_ROOT}/lib" \
-D TPL_HDF5_LIBRARIES:FILEPATH="${HDF5_LIBS}" \
-D TPL_ENABLE_Netcdf:BOOL=ON \
-D Netcdf_INCLUDE_DIRS:FILEPATH="${NETCDF_ROOT}/include" \
-D TPL_Netcdf_LIBRARIES:FILEPATH="${NETCDF_LIBS};${NETCDF_LIBS}" \
-D TPL_ENABLE_yaml-cpp:BOOL=ON \
-D yaml-cpp_LIBRARY_DIRS="${YAMLCPP_ROOT}/lib" \
-D KOKKOS_ARCH="Power8;Kepler37" \
$TRILINOS_DIR
```
## Your Environment
on WHITE
```
module load devpack/20180521/openmpi/3.1.0/gcc/7.2.0/cuda/9.2.88
module load yamlcpp/0.5.3/gcc/7.2.0
```
<!---
Include relevant details about your environment such that we can replicate this
issue.
-->
- **Relevant repo SHA1s:**
- **Relevant configure flags or configure script:**
- **Operating system and version:**
- **Compiler and TPL versions:**
Keep promoted "ATDM" builds of Trilinos cleanhttps://gitlab.osti.gov/jmwille/Trilinos/-/issues/3288SEACASExodus tests failing in new cuda 9.2 ATDM build on white/ride2018-11-30T03:12:47ZJames WillenbringSEACASExodus tests failing in new cuda 9.2 ATDM build on white/ride*Created by: fryeguy52*
CC: @trilinos/seacas , @kddevin (Trilinos Data Services Product Lead), @gsjaardema , @bartlettroscoe
## Next Action Status
PR #3418 which switched from module `netcdf-exo/4.6.1/openmpi/3.1.0/gcc/7.2.0/cu...*Created by: fryeguy52*
CC: @trilinos/seacas , @kddevin (Trilinos Data Services Product Lead), @gsjaardema , @bartlettroscoe
## Next Action Status
PR #3418 which switched from module `netcdf-exo/4.6.1/openmpi/3.1.0/gcc/7.2.0/cuda/9.2.88` to `netcdf/4.6.1/openmpi/3.1.0/gcc/7.2.0/cuda/9.2.88` on white/ride merged on 9/10/2018 and SEACAS tests fully passed on 9/11/2018.
## Description
As shown in [this query](https://testing-vm.sandia.gov/cdash/queryTests.php?project=Trilinos&filtercombine=and&filtercombine=and&filtercombine=and&date=2018-08-11&filtercombine=and&filtercombine=and&filtercombine=and&filtercombine=and&filtercombine=and&filtercombine=and&filtercombine=and&filtercombine=and&filtercombine=and&filtercount=4&showfilters=1&filtercombine=and&field1=buildname&compare1=65&value1=Trilinos-atdm-white-ride-cuda-9.2-&field2=buildname&compare2=64&value2=Trilinos-atdm-white-ride-cuda-9.2-debug-pt&field3=testname&compare3=63&value3=SEACAS&field4=status&compare4=62&value4=Passed) the tests:
* SEACASExodus_exodus_unit_tests
* SEACASExodus_exodus_unit_tests_nc5_env
are failing in the builds:
* Trilinos-atdm-white-ride-cuda-9.2-opt
* Trilinos-atdm-white-ride-cuda-9.2-debug
The output looks similar to what we were seeing in #2815
```
================================================================================
TEST_0
Running: "/bin/bash" "/home/jenkins/white/workspace/Trilinos-atdm-white-ride-cuda-9.2-opt/SRC_AND_BUILD/BUILD/packages/seacas/libraries/exodus/test/testall" "netcdf5"
Writing output to file "/home/jenkins/white/workspace/Trilinos-atdm-white-ride-cuda-9.2-opt/SRC_AND_BUILD/BUILD/packages/seacas/libraries/exodus/test/exodus_unit_tests.out"
--------------------------------------------------------------------------------
testwt - single precision write test...
Exodus Library Warning/Error: [ex_put_name]
ERROR: element block id 10 not found in file id 65536
testrd - single precision read test...
```
...
```
--------------------------------------------------------------------------------
TEST_1: Return code = 1
TEST_1: Pass criteria = Zero return code [FAILED]
TEST_1: Result = FAILED
================================================================================
OVERALL FINAL RESULT: TEST FAILED (SEACASExodus_exodus_unit_tests_nc5_env)
```
in that issue `SEACASExodus_exodus_unit_tests` was also failing on mutrino and we ended up disabling the test for that build.
## Steps to Reproduce
One should be able to reproduce this failure on the machine `white` as described in:
* https://github.com/trilinos/Trilinos/blob/develop/cmake/std/atdm/README.md
More specifically, the commands given for the system `white` are provided at:
* https://github.com/trilinos/Trilinos/blob/develop/cmake/std/atdm/README.md#ridewhite
The exact commands to reproduce this issue should be:
```
$ cd <some_build_dir>/
$ source $TRILINOS_DIR/cmake/std/atdm/load-env.sh cuda-9.2-opt
$ cmake \
-GNinja \
-DTrilinos_CONFIGURE_OPTIONS_FILE:STRING=cmake/std/atdm/ATDMDevEnv.cmake \
-DTrilinos_ENABLE_TESTS=ON -DTrilinos_ENABLE_SEACAS=ON \
$TRILINOS_DIR
$ make NP=16
$ bsub -x -Is -q rhel7F -n 16 ctest -j16
```Keep promoted "ATDM" builds of Trilinos cleanhttps://gitlab.osti.gov/jmwille/Trilinos/-/issues/3214seacas missing files.2018-08-22T15:17:31ZJames Willenbringseacas missing files.*Created by: VictorEijkhout*
A recent clone of the repository contains:
```
lrwxrwxrwx build/G-25072 0 2018-07-30 12:44 trilinos-git/packages/seacas/libraries/exodus/topology -> ../../../../docs/topology
lrwxrwxrwx build/G-250...*Created by: VictorEijkhout*
A recent clone of the repository contains:
```
lrwxrwxrwx build/G-25072 0 2018-07-30 12:44 trilinos-git/packages/seacas/libraries/exodus/topology -> ../../../../docs/topology
lrwxrwxrwx build/G-25072 0 2018-07-30 12:44 trilinos-git/packages/seacas/libraries/ioss/html -> ../../../../docs/ioss_html
lrwxrwxrwx build/G-25072 0 2018-07-30 12:44 trilinos-git/packages/seacas/libraries/exodus/html -> ../../../../docs/html
```
All three don't exist. This trips up rpmbuild, which is what I use for making installations, since it checks that all claimed files actually exist.
Please fix?
Victor.https://gitlab.osti.gov/jmwille/Trilinos/-/issues/3183New SEACAS tests failing in ATDM Trilinos builds starting on 7/19/2018 and 7/...2018-11-30T03:12:46ZJames WillenbringNew SEACAS tests failing in ATDM Trilinos builds starting on 7/19/2018 and 7/23/2018*Created by: bartlettroscoe*
New SEACAS tests failing in ATDM Trilinos builds starting on 7/19/2018 and 7/23/2018
CC: @trilinos/seacas, @gsjaardema (pushed breaking commits?), @kddevin (Trilinos Data Services Product Lead)
## Next...*Created by: bartlettroscoe*
New SEACAS tests failing in ATDM Trilinos builds starting on 7/19/2018 and 7/23/2018
CC: @trilinos/seacas, @gsjaardema (pushed breaking commits?), @kddevin (Trilinos Data Services Product Lead)
## Next Action Status
PR #3213 merged on 8/1/2018 then later fixed in PR #3251 merged 8/8/2018 that disabled most of these tests in the 'mutrino' builds on 8/2/2018. No test failures since 8/8/2018 as of 8/29/2018.
## Description
As shown in [this query for the builds today](https://testing-vm.sandia.gov/cdash/queryTests.php?project=Trilinos&date=2018-07-24&filtercombine=and&filtercombine=and&filtercount=5&showfilters=1&filtercombine=and&field1=buildname&compare1=65&value1=Trilinos-atdm-&field2=status&compare2=62&value2=passed&field3=status&compare3=62&value3=notrun&field4=groupname&compare4=61&value4=ATDM&field5=testname&compare5=65&value5=SEACAS), the tests:
* SEACASAprepro_aprepro_array_test
* SEACASAprepro_aprepro_command_line_include_test
* SEACASAprepro_aprepro_command_line_vars_test
* SEACASAprepro_aprepro_unit_test
* SEACASAprepro_lib_aprepro_lib_array_test
* SEACASAprepro_lib_aprepro_lib_unit_test
* SEACASExodus_exodus_unit_tests_nc5_env
are failing in the builds:
* Trilinos-atdm-mutrino-intel-debug-openmp
* Trilinos-atdm-mutrino-intel-opt-openmp
and the tests:
* SEACASIoss_exodus32_to_exodus32
* SEACASIoss_exodus32_to_exodus32_pnetcdf
* SEACASIoss_exodus32_to_exodus64
are failing in the builds:
* Trilinos-atdm-hansen-shiller-cuda-8.0-debug
* Trilinos-atdm-hansen-shiller-cuda-8.0-opt
As shown in [this query showing failing SEACAS tests going back to 7/10/2018](https://testing-vm.sandia.gov/cdash/queryTests.php?project=Trilinos&date=2018-07-24&filtercombine=and&filtercombine=and&filtercombine=and&filtercombine=and&filtercombine=and&filtercombine=and&filtercount=6&showfilters=1&filtercombine=and&field1=buildname&compare1=65&value1=Trilinos-atdm-&field2=status&compare2=62&value2=passed&field3=status&compare3=62&value3=notrun&field4=groupname&compare4=61&value4=ATDM&field5=testname&compare5=65&value5=SEACAS&field6=buildstarttime&compare6=83&value6=2018-07-10), the test ` SEACASExodus_exodus_unit_tests_nc5_env` started failing on 7/19/2018 and the other tests started failing on 7/23/2018. There were several PRs merged the days before these dates by @gsjaardema so it is not clear which changes caused these new failures but it seems likely that one or more of the commits in these merged PRs triggered these new failures.
Also, the test `SEACASAprepro_aprepro_test_dump_reread` added in one of these PRs appeared on 7/23/2018 and then started randomly failing as shown in [this query](https://testing-vm.sandia.gov/cdash/queryTests.php?project=Trilinos&date=2018-08-02&filtercombine=and&filtercombine=and&filtercount=5&showfilters=1&filtercombine=and&field1=buildname&compare1=65&value1=Trilinos-atdm-&field2=groupname&compare2=61&value2=ATDM&field3=testname&compare3=61&value3=SEACASAprepro_aprepro_test_dump_reread&field4=site&compare4=61&value4=mutrino&field5=buildstarttime&compare5=83&value5=2018-07-15). When the test passes like shown [here](https://testing-vm.sandia.gov/cdash/testDetails.php?test=51055647&build=3759381), it shows:
```
================================================================================
TEST_3
Running: "diff" "-w" "test-filter.dump" "test-reread.dump"
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
TEST_3: Return code = 0
TEST_3: Pass criteria = Zero return code [PASSED]
TEST_3: Result = PASSED
================================================================================
```
when it fails like shown [here](https://testing-vm.sandia.gov/cdash/testDetails.php?test=51563099&build=3790512), it shows:
```
================================================================================
TEST_3
Running: "diff" "-w" "test-filter.dump" "test-reread.dump"
--------------------------------------------------------------------------------
1,2c1,2
< Thu Aug 2 11:20:16 2018: [unset]:_pmi_alps_init:alps_get_placement_info returned with error -1
< Thu Aug 2 11:20:16 2018: [unset]:_pmi_init:_pmi_alps_init returned -1
---
> Thu Aug 2 11:20:17 2018: [unset]:_pmi_alps_init:alps_get_placement_info returned with error -1
> Thu Aug 2 11:20:17 2018: [unset]:_pmi_init:_pmi_alps_init returned -1
--------------------------------------------------------------------------------
TEST_3: Return code = 1
TEST_3: Pass criteria = Zero return code [FAILED]
TEST_3: Result = FAILED
================================================================================
```
## Steps to reproduce
These failures should be reproducable on the machines 'hansen' or 'shiller' and 'mutrino' using the instructions in:
* https://github.com/trilinos/Trilinos/blob/develop/cmake/std/atdm/README.md
For example, for the failures on 'hansen'/'shiler', the specific instructions are given at:
* https://github.com/trilinos/Trilinos/blob/develop/cmake/std/atdm/README.md#shillerhansen
For example, after cloning Trilinos, the following commands should reproduce the test failures on 'hansen' or 'shiller' with:
```
$ cd <some_build_dir>/
$ source $TRILINOS_DIR/cmake/std/atdm/load-env.sh cuda-8.0-debug
$ cmake \
-GNinja \
-DTrilinos_CONFIGURE_OPTIONS_FILE:STRING=cmake/std/atdm/ATDMDevEnvSettings.cmake \
-DTrilinos_ENABLE_TESTS=ON -DTrilinos_ENABLE_SEACAS=ON \
$TRILINOS_DIR
$ make NP=16
$ srun ctest -j16
```
Keep promoted "ATDM" builds of Trilinos cleanhttps://gitlab.osti.gov/jmwille/Trilinos/-/issues/2989seacas: -qfixed must be applied when building with XL Fortran2018-06-21T14:37:50ZJames Willenbringseacas: -qfixed must be applied when building with XL Fortran*Created by: djfitzgerald*
@trilinos/seacas
## Expectations
Default cmake configuration should produce a version of seacas that builds under IBM XL Fortran
## Current Behavior
The version of seacas produced by the default cmake ...*Created by: djfitzgerald*
@trilinos/seacas
## Expectations
Default cmake configuration should produce a version of seacas that builds under IBM XL Fortran
## Current Behavior
The version of seacas produced by the default cmake configuration contains a number of errors of the form `1515-019 (S) Syntax is incorrect` and `1515-002 (S) END card is missing`.
## Motivation and Context
My team was working with LLNL to assist in their testing the installation of Trilinos under [Spack](https://spack.io/). We developed a patch that Spack automatically applies to all versions of the Trilinos source code beginning with 12.10.1 when building with the XL compiler suite (or at least using XL Fortran). This patch adds the `-qfixed` option to the XL compiler line in `pacakges/seacas/cmake/FortranSettings.cmake`. As this is patching what appears to be a Trilinos problem, I feel that this fix should be made into the Trilinos source code.
## Definition of Done
When attempting to compile Trilinos with the XL compiler suite, seacas should compile successfully.
## Possible Solution
See attached patch file under "Additional Information" section
## Steps to Reproduce
1. On a test system, install version the IBM XL compiler suite, IBM ESSL, LAPACK 3.4.2, and Spectrum MPI
2. Download a *.zip archive of the Trilinos `develop` branch through GitHub with `wget https://github.com/trilinos/Trilinos/archive/develop.zip`
3. Unzip the archive: `unzip develop.zip`
4. FTP a copy of the patch xlf_seacas.patch to my home directory.
5. Create an installation directory for Trilinos: `cd ~/ ; mkdir Trilinos`
7. Download and installed the following Trilinos dependencies into your home directory:
a. cmake-3.11.3
b. hdf5-1.10.2, installed into `$HOME/hdf5` and symlinked into `$HOME/hdf5-1.10.2/hdf5`)
c. netcdf-4.6.1, configured with the command `CPPFLAGS=-I$HOME/hdf5/include LDFLAGS=-L$HOME/hdf5/lib ./configure --prefix=$HOME/netcdf`
8. `cd` into `$HOME/Trilinos`
9. Issue the following `cmake` command:
```
/$HOME/cmake-3.11.3/bin/cmake \
-DCMAKE_C_COMPILER=/usr/bin/xlc_r \
-DCMAKE_CXX_COMPILER=/usr/bin/xlc++_r \
-DCMAKE_Fortran_COMPILER=/usr/bin/xlf2008_r \
-DTPL_ENABLE_MPI=ON \
-DTPL_BLAS_LIBRARIES='/opt/ibmmath/essl/6.1/lib64/libessl.so;/opt/ibmmath/essl/6.1/lib64/libessl6464.so;/opt/ibmmath/essl/6.1/lib64/libesslsmp6464.so;/opt/ibmmath/essl/6.1/lib64/libesslsmpcuda.so;/opt/ibmmath/essl/6.1/lib64/libesslsmp.so' \
-DTPL_LAPACK_LIBRARIES='/usr/lib64/liblapacke.so.3.4.2;/usr/lib64/liblapack.so.3.4.2' \
-DNetcdf_LIBRARY_DIRS='$HOME/netcdf/lib' \
-DTPL_Netcdf_INCLUDE_DIRS='$HOME/netcdf/include' \
-DMPI_BASE_DIR=/opt/ibm/spectrum_mpi \
-DTrilinos_ENABLE_ALL_PACKAGES=ON \
-DTPL_ENABLE_Matio=OFF \
-DTPL_ENABLE_X11=OFF \
-DTrilinos_ENABLE_TESTS:BOOL=ON \
-DTrilinos_ENABLE_EXAMPLES:BOOL=ON \
-DTrilinos_ENABLE_CXX11:BOOL=ON \
-DTrilinos_CXX11_FLAGS:STRING=-std=gnu++11 \
-DCMAKE_INSTALL_PREFIX=$HOME/Trilinos \
$HOME/Trilinos-fix-2781
```
9. Execute `export INCLUDE_PATH=$INCLUDE_PATH:/opt/ibm/spectrum_mpi/include/:$HOME/netcdf/include/`
10. Execute `make -j install`
11. Verify that seacas was unable to compile because of the reasons described above.
## Your Environment
- Have confirmed it with Trilinos 12.12.1 from git (SHA ecd4606fa332212433c98bf950a69cc7), also with newer Trilinos versions (including recent `develop` branch)
- Operating system was RHEL 7.4 on an IBM Power9 system.
- IBM XL 16.1 compiler suite
- `cmake` 3.11.3
- `hdf5` 1.10.2
- `netcdf` 4.6.1
- LAPACK 3.4.2
- IBM Spectrum MPI
## Related Issues
* Related to #2781
## Additional Information
<!---
Anything else that might be helpful for us to know in addressing this issue:
* Configure log file:
* Build log file:
* Test log file:
* When was the last time everything worked (date/time; SHA1s; etc.)?
* What did you do that made the bug rear its ugly head?
* Have you tried turning it off and on again?
-->
* Build log file: [build.log](https://github.com/trilinos/Trilinos/files/2119741/build.log)
* Patch to fix: [xlf_seacas.patch.txt](https://github.com/trilinos/Trilinos/files/2119746/xlf_seacas.patch.txt)
https://gitlab.osti.gov/jmwille/Trilinos/-/issues/2815SEACAS tests failing in ATDM builds on mutrino2018-11-30T03:12:46ZJames WillenbringSEACAS tests failing in ATDM builds on mutrino*Created by: fryeguy52*
CC: @bartlettroscoe, @trilinos/seacas
## Next Action Status
Switching from 'salloc' to 'sbatch' eliminated all but one of the failing tests and the remaining failing test `SEACASExodus_exodus_unit_tests` wa...*Created by: fryeguy52*
CC: @bartlettroscoe, @trilinos/seacas
## Next Action Status
Switching from 'salloc' to 'sbatch' eliminated all but one of the failing tests and the remaining failing test `SEACASExodus_exodus_unit_tests` was disabled in commit d12ca4ebe37d9712574fa8e98fa25eca5acb5422 merged to 'develop' in PR #3011 on 6/26/2018.
## Summary
The following tests are failing in the nightly jenkins jobs of the ATDM configuration on mutrino
[SEACASAprepro_aprepro_command_line_include_test](https://testing.sandia.gov/cdash/testDetails.php?test=48123101&build=3591754)
[SEACASAprepro_aprepro_command_line_vars_test](https://testing.sandia.gov/cdash/testDetails.php?test=48123100&build=3591754)
[SEACASAprepro_aprepro_unit_test](https://testing.sandia.gov/cdash/testDetails.php?test=48123098&build=3591754)
[SEACASAprepro_lib_aprepro_lib_array_test](https://testing.sandia.gov/cdash/testDetails.php?test=48123102&build=3591754)
[SEACASAprepro_lib_aprepro_lib_unit_test](https://testing.sandia.gov/cdash/testDetails.php?test=48123103&build=3591754)
[SEACASExodus_exodus_unit_tests](https://testing.sandia.gov/cdash/testDetails.php?test=48363282&build=3591754)
The list of failures can be seen [here](https://testing.sandia.gov/cdash/queryTests.php?project=Trilinos&date=2018-05-23&limit=0&filtercount=2&showfilters=1&filtercombine=and&field1=testname&compare1=63&value1=SEACASA&field2=site&compare2=61&value2=mutrino) on CDash
They are failing in both
[Trilinos-atdm-mutrino-intel-opt-openmp](https://testing.sandia.gov/cdash/index.php?project=Trilinos&parentid=3590846)
[Trilinos-atdm-mutrino-intel-debug-openmp](https://testing.sandia.gov/cdash/index.php?project=Trilinos&parentid=3591410)
It looks like they all have something like this in the error output:
```
TEST_2
Running: "diff" "-w" "/lscratch1/jenkins/mutrino-slave/workspace/Trilinos-atdm-mutrino-intel-opt-openmp/SRC_AND_BUILD/Trilinos/packages/seacas/libraries/aprepro_lib/test_standard.out" "/lscratch1/jenkins/mutrino-slave/workspace/Trilinos-atdm-mutrino-intel-opt-openmp/SRC_AND_BUILD/BUILD/packages/seacas/libraries/aprepro_lib/test.output"
--------------------------------------------------------------------------------
diff: /lscratch1/jenkins/mutrino-slave/workspace/Trilinos-atdm-mutrino-intel-opt-openmp/SRC_AND_BUILD/BUILD/packages/seacas/libraries/aprepro_lib/test.output: No such file or directory
--------------------------------------------------------------------------------
TEST_2: Return code = 2
TEST_2: Pass criteria = Zero return code [FAILED]
TEST_2: Result = FAILED
```
## Steps to Reproduce
on mutrino clone Trilinos and run the following. This will automatically set up the environment.
```
$ cd <some_build_dir>/
$ source $TRILINOS_DIR/cmake/std/atdm/load-env.sh intel-opt-openmp
$ 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
```
## Environment
This is set up automatically in the instructions to reproduce above
Initial cleanup of new ATDM builds of Trilinoshttps://gitlab.osti.gov/jmwille/Trilinos/-/issues/2789Work-around for IBM xlC bug (was called "Attempt to intialize matrix in heade...2018-06-18T16:10:39ZJames WillenbringWork-around for IBM xlC bug (was called "Attempt to intialize matrix in header file fails under IBM xlC")*Created by: djfitzgerald*
When attempting to unit test a fix I've been working on for #2781, the IBM XL compiler fails at [packages/seacas/libraries/ioss/src/generated/Iogn_GeneratedMesh.h:493](https://github.com/trilinos/Trilinos/blo...*Created by: djfitzgerald*
When attempting to unit test a fix I've been working on for #2781, the IBM XL compiler fails at [packages/seacas/libraries/ioss/src/generated/Iogn_GeneratedMesh.h:493](https://github.com/trilinos/Trilinos/blob/3cc0152887609df06f04477ce483bca090fdab45/packages/seacas/libraries/ioss/src/generated/Iogn_GeneratedMesh.h#L493) with `error: 1540-2991 The expression is not supported.` The failing expression is as follows:
```
double rotmat[3][3]{};
```
This change was added since 12.12.1, and I don't know what its purpose was so I am loath to "fix" it. I am building Trilinos from Spack, using a Spack repository to recognize a fake Trilinos "version 12.13.1" that points to a working branch in my fork of this GitHub repository. From the hacked Spack `package.py` file for my local Trilinos install:
```
version('12.13.1',
git='https://github.com/basicmanfitz/Trilinos.git', branch='fix-2781')
```
My Spack install command is:
```
spack install --test=root trilinos@12.13.1%xl_r ~pnetcdf ^netlib-lapack+external-blas ^netcdf%gcc ^m4%gcc
```
And the pertinent text from my Spack build log:
```
7271 cd /tmp/danfitz/spack-stage/spack-stage-g_hy3L/Trilinos/spack-build/packages/teuchos/comm/src && /opt/ibm/spectrum_mpi/bin/mpixlC -+ -DTEUCHOSCOMM_LIB_E
XPORTS_MODE -Dteuchoscomm_EXPORTS -I/tmp/danfitz/spack-stage/spack-stage-g_hy3L/Trilinos/spack-build -I/u/danfitz/spack/var/spack/stage/trilinos-12.13.1
-c4ai2lelm44crs4zncdh35bylpr766h6/Trilinos/packages/teuchos/comm/src -I/u/danfitz/spack/var/spack/stage/trilinos-12.13.1-c4ai2lelm44crs4zncdh35bylpr766h
6/Trilinos/packages/teuchos/parameterlist/src -I/u/danfitz/spack/var/spack/stage/trilinos-12.13.1-c4ai2lelm44crs4zncdh35bylpr766h6/Trilinos/packages/teu
chos/parser/src -I/tmp/danfitz/spack-stage/spack-stage-g_hy3L/Trilinos/spack-build/packages/teuchos/core/src -I/u/danfitz/spack/var/spack/stage/trilinos
-12.13.1-c4ai2lelm44crs4zncdh35bylpr766h6/Trilinos/packages/teuchos/core/src -I/tmp/danfitz/spack-stage/spack-stage-g_hy3L/Trilinos/spack-build/packages
/kokkos/core/src -I/u/danfitz/spack/var/spack/stage/trilinos-12.13.1-c4ai2lelm44crs4zncdh35bylpr766h6/Trilinos/packages/kokkos/core/src -I/u/danfitz/spa
ck/opt/spack/linux-rhel7-ppc64le/xl_r-16.1/boost-1.67.0-5bom5du2myssl3gywvnxdzxhurklibbg/include -DMUMPS_5_0 -std=c++11 -g -qpic -o CMakeFiles/teucho
scomm.dir/Teuchos_YamlParameterListHelpers.cpp.o -c /u/danfitz/spack/var/spack/stage/trilinos-12.13.1-c4ai2lelm44crs4zncdh35bylpr766h6/Trilinos/packages
/teuchos/comm/src/Teuchos_YamlParameterListHelpers.cpp
7272 In file included from /u/danfitz/spack/var/spack/stage/trilinos-12.13.1-c4ai2lelm44crs4zncdh35bylpr766h6/Trilinos/packages/seacas/libraries/ioss/src/gen
erated/Iogn_GeneratedMesh.C:39:
>> 7273 /u/danfitz/spack/var/spack/stage/trilinos-12.13.1-c4ai2lelm44crs4zncdh35bylpr766h6/Trilinos/packages/seacas/libraries/ioss/src/generated/Iogn_GeneratedM
esh.h:493:44: error: 1540-2991 The expression is not supported.
7274 double rotmat[3][3]{};
7275 ^
7276 1 error generated.
>> 7277 Error while processing /u/danfitz/spack/var/spack/stage/trilinos-12.13.1-c4ai2lelm44crs4zncdh35bylpr766h6/Trilinos/packages/seacas/libraries/ioss/src/ge
nerated/Iogn_GeneratedMesh.C.
>> 7278 make[2]: *** [packages/seacas/libraries/ioss/src/generated/CMakeFiles/Iogn.dir/Iogn_GeneratedMesh.C.o] Error 1
7279 make[2]: *** Waiting for unfinished jobs....
7280 make[2]: Leaving directory `/tmp/danfitz/spack-stage/spack-stage-g_hy3L/Trilinos/spack-build'
>> 7281 make[1]: *** [packages/seacas/libraries/ioss/src/generated/CMakeFiles/Iogn.dir/all] Error 2
```https://gitlab.osti.gov/jmwille/Trilinos/-/issues/2720Seacas: Remove calls to deprecated Kokkos::View methods2018-08-22T15:21:40ZJames WillenbringSeacas: Remove calls to deprecated Kokkos::View methods*Created by: mhoemmen*
Tracking issue filed in Seacas repository: https://github.com/gsjaardema/seacas/issues/106
@trilinos/seacas @micahahoward @prwolfe @rrdrake *Created by: mhoemmen*
Tracking issue filed in Seacas repository: https://github.com/gsjaardema/seacas/issues/106
@trilinos/seacas @micahahoward @prwolfe @rrdrake https://gitlab.osti.gov/jmwille/Trilinos/-/issues/2650SEACAS tests failing in ATDM CUDA builds starting 4/26/20182018-11-30T03:12:46ZJames WillenbringSEACAS tests failing in ATDM CUDA builds starting 4/26/2018*Created by: bartlettroscoe*
**CC:** @trilinos/seacas, @gsjaardema, @fryeguy52
## Next Action Status
Updated SEACAS is also causing mesh reading problems on non-CUDA builds for larger numbers of MPI ranks. PR #2653 was merged on...*Created by: bartlettroscoe*
**CC:** @trilinos/seacas, @gsjaardema, @fryeguy52
## Next Action Status
Updated SEACAS is also causing mesh reading problems on non-CUDA builds for larger numbers of MPI ranks. PR #2653 was merged on 4/27/2018. which reverts PR #2625 updating SEACAS. New issue will be opened if next SEACAS snapshot cause an error.
## Description
As shown in the query:
* https://testing-vm.sandia.gov/cdash/queryTests.php?project=Trilinos&date=2018-04-26&filtercombine=and&filtercombine=and&filtercombine=and&filtercount=4&showfilters=1&filtercombine=and&field1=buildname&compare1=65&value1=Trilinos-atdm-&field2=status&compare2=62&value2=passed&field3=status&compare3=62&value3=notrun&field4=testname&compare4=65&value4=SEACAS
The SEACAS tests:
* `SEACASIoss_exodus32_to_exodus32`
* `SEACASIoss_exodus32_to_exodus32_pnetcd`
* `SEACASIoss_exodus32_to_exodus64`
are failling in all of the current [ATDM Trilinos](https://snl-wiki.sandia.gov/display/CoodinatedDevOpsATDM/ATDM+Builds+of+Trilinos) CUDA builds:
* `Trilinos-atdm-hansen-shiller-cuda-debug`
* `Trilinos-atdm-hansen-shiller-cuda-opt`
* `Trilinos-atdm-white-ride-cuda-debug`
* `Trilinos-atdm-white-ride-cuda-opt`
This was likely due to the update of SEACAS into Trilinos in the commit 89d48adf7ff7f919fefaf035f228a01947c9a5aa merged in the PR #2625 .
## Steps to Reproduce
One should be able to reproduce these failing tests on the machines `white` (SON), `ride` (SRN), `hansen` (SON), or `shiller` (SRN) as described in:
* https://github.com/trilinos/Trilinos/blob/develop/cmake/std/atdm/README.md
For example, on `white` one should be able to reproduce these failing tests with:
```
$ cd <some_build_dir>/
$ source $TRILINOS_DIR/cmake/std/atdm/load-env.sh cuda-debug
$ cmake \
-GNinja \
-DTrilinos_CONFIGURE_OPTIONS_FILE:STRING=cmake/std/atdm/ATDMDevEnv.cmake \
-DTrilinos_ENABLE_TESTS=ON -DTrilinos_ENABLE_SEACAS=ON \
$TRILINOS_DIR
$ make NP=16
$ bsub -x -Is -q rhel7F -n 16 ctest -j16
```
Keep promoted "ATDM" builds of Trilinos cleanhttps://gitlab.osti.gov/jmwille/Trilinos/-/issues/2359'#line 1' from flex generated apr_scanner.cpp SEACAS file causing unnecessary...2018-11-30T03:12:46ZJames Willenbring'#line 1' from flex generated apr_scanner.cpp SEACAS file causing unnecessary rebuilds when using Ninja + CUDA-8*Created by: bartlettroscoe*
**CC:** @trilinos/seacas, @fryeguy52
## Description
The following line in the SEACAS file:
```
packages/seacas/libraries/aprepro_lib/apr_scanner.cc:974:#line 1 "/scratch/gdsjaar/seacas/packages/sea...*Created by: bartlettroscoe*
**CC:** @trilinos/seacas, @fryeguy52
## Description
The following line in the SEACAS file:
```
packages/seacas/libraries/aprepro_lib/apr_scanner.cc:974:#line 1 "/scratch/gdsjaar/seacas/packages/seacas/libraries/aprepro_lib/aprepro.ll"
```
is causing the ninja CUDA build for Trilinos with SEACAS to rebuild the same files every time, even when everything should be up-to-date.
The cause for this is very strange. There is a defect with the `nvcc` program (at least CUDA 8.0.61) when running `nvcc -M -Wno-deprecated-gpu-targets` on a file that has `#line 1 <some-file>` in the file results in `nvcc` incorrectly spitting out a dependency on `<some-file>`. This results in `nvcc` when run under `nvcc_wrapper` run under ninja to produce a dependency on the file `<some-file>`. Apparently this does not happen for any number other than `1`. For example, lines with `#line 2 <some-file>` do not cause `nvcc` to print out a bad dependency.
Kitware reported this NVIDIA as bug number 2080680 just today. (However, their issue tracker is not public).
The workaround for this is to make the single one-line change:
```
diff --git a/packages/seacas/libraries/aprepro_lib/apr_scanner.cc b/packages/seacas/libraries/aprepro_lib/apr_scanner.cc
index 747470a..a2512cd 100644
--- a/packages/seacas/libraries/aprepro_lib/apr_scanner.cc
+++ b/packages/seacas/libraries/aprepro_lib/apr_scanner.cc
@@ -971,7 +971,6 @@ static yyconst flex_int16_t yy_rule_linenum[102] = {
#define yymore() yymore_used_but_not_detected
#define YY_MORE_ADJ 0
#define YY_RESTORE_YY_MORE_OFFSET
-#line 1 "/scratch/gdsjaar/seacas/packages/seacas/libraries/aprepro_lib/aprepro.ll"
/* -*- Mode: c++ -*- */
#line 39 "/scratch/gdsjaar/seacas/packages/seacas/libraries/aprepro_lib/aprepro.ll"
```
Also, changing `#line 1 <file-name>` to `#line 2 <file-name>` also fixes the problem.
## Steps to Reproduce
This can be produced, for example, with one of the ATDM Trilinos CUDA configurations described at:
* https://github.com/trilinos/Trilinos/blob/develop/cmake/std/atdm/README.md
For example, just log onto `hansen` or `shiller` or `white` or `ride`, clone Trilinos somewhere, and then configure and build with:
```
cd <some_build_dir>/
$ source $TRILINOS_DIR/cmake/std/atdm/load-env.sh cuda-opt
$ cmake \
-GNinja \
-DTrilinos_CONFIGURE_OPTIONS_FILE:STRING=cmake/std/atdm/ATDMDevEnv.cmake \
-DTrilinos_ENABLE_Panzer=ON -DPanzer_ENABLE_TESTS=ON \
$TRILINOS_DIR
$ ninja -j16 # Builds everything the first time
$ ninja -j16 # Rebuilds a bunch of targets!
```
You can see what is triggering the rebuild using:
```
$ ninja -d explain
...
ninja explain: output /scratch/gdsjaar/seacas/packages/seacas/libraries/aprepro_lib/aprepro.ll of phony edge with no inputs doesn't exist
ninja explain: /scratch/gdsjaar/seacas/packages/seacas/libraries/aprepro_lib/aprepro.ll is dirty
ninja explain: packages/seacas/libraries/aprepro_lib/CMakeFiles/aprepro_lib.dir/apr_scanner.cc.o is dirty
...
$ ninja -t deps packages/seacas/libraries/aprepro_lib/CMakeFiles/aprepro_lib.dir/apr_scanner.cc.o
...
/scratch/gdsjaar/seacas/packages/seacas/libraries/aprepro_lib/aprepro.ll
...
```
See, that file `/scratch/gdsjaar/seacas/packages/seacas/libraries/aprepro_lib/aprepro.ll` is not on this system obviously.
Then to fix, just apply the patch shown above, rebuild once and then rebuild again, and you will get:
```
$ time ninja
ninja: no work to do.
real 0m2.744s
user 0m0.275s
sys 0m0.218s
```
(Yes, that is ninja evaluating all of the targets to figure out if it needs to build any of the Panzer tests in under 3 sec! That is why we want to be able to use ninja.)
https://gitlab.osti.gov/jmwille/Trilinos/-/issues/2100Configuration fails: CMake Error: CMake can not determine linker language for...2018-08-22T15:19:35ZJames WillenbringConfiguration fails: CMake Error: CMake can not determine linker language for target: blotlib*Created by: yurivict*
This error occurs when ```-DTPL_ENABLE_Netcdf=ON```:
```
-- Configuring done
CMake Error: CMake can not determine linker language for target: blotlib
CMake Error: CMake can not determine linker language for ...*Created by: yurivict*
This error occurs when ```-DTPL_ENABLE_Netcdf=ON```:
```
-- Configuring done
CMake Error: CMake can not determine linker language for target: blotlib
CMake Error: CMake can not determine linker language for target: blotlib
CMake Error in packages/seacas/applications/blot/CMakeLists.txt:
Exporting the target "blotlib" is not allowed since its linker language
cannot be determined
```
Version: 12-12-1 on FreeBSD 11.1
https://gitlab.osti.gov/jmwille/Trilinos/-/issues/2042SEACAS Tests Failing on Clean Track2017-12-05T17:27:11ZJames WillenbringSEACAS Tests Failing on Clean Track*Created by: william76*
<!--- Provide a general summary of the issue in the Title above. -->
There are 3 SEACAS tests failing on the nightlies (https://testing.sandia.gov/cdash/viewTest.php?onlyfailed&buildid=3253872)
- [SEACASAprepro...*Created by: william76*
<!--- Provide a general summary of the issue in the Title above. -->
There are 3 SEACAS tests failing on the nightlies (https://testing.sandia.gov/cdash/viewTest.php?onlyfailed&buildid=3253872)
- [SEACASAprepro_aprepro_unit_test](https://testing.sandia.gov/cdash/testDetails.php?test=43150010&build=3254222)
- [SEACASExodus_exodus_unit_tests](https://testing.sandia.gov/cdash/testDetails.php?test=43188945&build=3254222)
- [SEACASExodus_exodus_unit_tests_nc5_env](https://testing.sandia.gov/cdash/testDetails.php?test=43188946&build=3254222)
@trilinos/seacas
## Expectations
Test failures on the CLEAN track block promotion from develop to master and thus should be fixed promptly.
## Related Issues
Possibly related to the commits that broke the CI builds on issue #2039 ?
## Additional Information
Console outputs on CDash:
- https://testing.sandia.gov/cdash/testDetails.php?test=43150010&build=3254222
- https://testing.sandia.gov/cdash/testDetails.php?test=43188945&build=3254222
- https://testing.sandia.gov/cdash/testDetails.php?test=43188946&build=3254222