Merge pull request #2625 from gsjaardema/seacas_github_snapshot

SEACAS: Automatic snapshot commit from seacas at 6909256b8
trilinos · Apr 25, 2018 · 1b19c57 · 1b19c57
2 parents aa0c96b + ee92d9b
commit 1b19c57
Show file tree

Hide file tree

Showing 3,228 changed files with 98,142 additions and 30,501 deletions.
diff --git a/packages/seacas/CMakeLists.txt b/packages/seacas/CMakeLists.txt
@@ -22,6 +22,58 @@ TRIBITS_ADD_OPTION_AND_DEFINE(
   OFF
   )
 
+function(disable_if_no_fortran package)
+IF (NOT ${PROJECT_NAME}_ENABLE_Fortran)
+  IF (${PROJECT_NAME}_ENABLE_SEACAS${package})
+    MESSAGE("-- "
+      "WARNING: Setting ${PROJECT_NAME}_ENABLE_SEACAS${package}=OFF"
+      " even though it was set to ${${PROJECT_NAME}_ENABLE_SEACAS${package}}"
+      " because ${PROJECT_NAME}_ENABLE_Fortran=OFF!"
+      )
+  ELSEIF("${${PROJECT_NAME}_ENABLE_SEACAS${package}}" STREQUAL "")
+     MESSAGE("-- "
+      "NOTE: Setting ${PROJECT_NAME}_ENABLE_SEACAS${package}=OFF"
+      " because ${PROJECT_NAME}_ENABLE_Fortran=OFF!"
+       )
+  ENDIF()
+  SET(${PROJECT_NAME}_ENABLE_SEACAS${package} OFF PARENT_SCOPE)
+ENDIF()
+endfunction()
+
+disable_if_no_fortran(Mapvarlib)
+disable_if_no_fortran(Exodus_for)
+disable_if_no_fortran(ExoIIv2for32)
+disable_if_no_fortran(Supes)
+disable_if_no_fortran(Suplib)
+disable_if_no_fortran(PLT)
+disable_if_no_fortran(Blot)
+disable_if_no_fortran(Fastq)
+disable_if_no_fortran(SVDI)
+disable_if_no_fortran(Algebra)
+disable_if_no_fortran(Exotxt)
+disable_if_no_fortran(Gjoin)
+disable_if_no_fortran(Gen3D)
+disable_if_no_fortran(Genshell)
+disable_if_no_fortran(Grepos)
+disable_if_no_fortran(Grope)
+disable_if_no_fortran(Mapvar)
+disable_if_no_fortran(Mapvar-kd)
+disable_if_no_fortran(Numbers)
+disable_if_no_fortran(Txtexo)
+disable_if_no_fortran(Ex2ex1v2)
+disable_if_no_fortran(Ex1ex2v2)
+
+IF (NOT ${PROJECT_NAME}_ENABLE_Fortran)
+# For some reason, this variable is undefined if fortran is disabled and it causes a cmake error.
+# define it to a nonsense variable to avoid error.
+  IF (NOT CMAKE_Fortran_LINK_EXECUTABLE)
+    MESSAGE("-- "
+      "WARNING: Setting CMAKE_Fortran_LINK_EXECUTABLE to a random value to avoid CMake error"
+      )
+    SET(CMAKE_Fortran_LINK_EXECUTABLE empty)
+  ENDIF()
+ENDIF()
+
 ASSERT_DEFINED(TPL_ENABLE_Pthread)
 IF (SEACASExodus_ENABLE_THREADSAFE AND NOT TPL_ENABLE_Pthread)
   MESSAGE(FATAL_ERROR "You set SEACASExodus_ENABLE_THREADSAFE=ON, but TriBITs support for Pthread(s) is not enabled (TPL_ENABLE_Pthread=OFF).  This is not allowed.  Please enable Pthreads before attempting to enable the thread-safe Exodus support.")

diff --git a/packages/seacas/IossProperties.md b/packages/seacas/IossProperties.md
@@ -5,6 +5,9 @@
  LOGGING   | on/[off] | enable/disable logging of field input/output
  LOWER_CASE_VARIABLE_NAMES | [on]/off | Convert all variable names on database to lowercase; replace ' ' with '_'
  USE_GENERIC_CANONICAL_NAMES | on/[off]  | use `block_{id}` as canonical name of an element block instead of the name (if any) stored on the database. The database name will be an alias.
+ ENABLE_FIELD_RECOGNITION | [on]/off | try to combine scalar fields with common basename and recognized suffix into vector, tensor, ...
+ FIELD_SUFFIX_SEPARATOR  | character ['_'] | use this suffix as separtor between field basename and suffices when recognizing fields
+ MINIMIZE_OPEN_FILES | on/[off] | If on, then close file after each timestep and then reopen on next output
 
 ## Auto-Decomposition-Related Properties
 
@@ -15,6 +18,7 @@ RESTART_DECOMPOSITION_METHOD | {method} | Decompose a DB with type `RESTART_IN`
 DECOMPOSITION_METHOD | {method} | Decompose all input DB using `method`
 PARALLEL_CONSISTENCY | [on]/off | On if the client will call Ioss functions consistently on all processors. If off, then the auto-decomp and auto-join cannot be used.
 RETAIN_FREE_NODES | [on]/off | In auto-decomp, will nodes not connected to any elements be retained. 
+LOAD_BALANCE_THRESHOLD | {real} [1.4] | CGNS-Structured only -- Load imbalance permitted Load on Proc / Avg Load
 
 ### Valid values for Decomposition Method
 
@@ -89,3 +93,4 @@ ENABLE_FILE_GROUPS | on/[off]   | experimental
  DECOMP_SHOW_PROGRESS | on/[off] | show memory and elapsed time during autodecomp.
  DECOMP_SHOW_HWM      | on/[off] | show high-water memory during autodecomp
  IOSS_TIME_FILE_OPEN_CLOSE | on/[off] | show elapsed time during parallel-io file open/close/create
+ CHECK_PARALLEL_CONSISTENCY | ignored | check Ioss::GroupingEntity parallel consistency
diff --git a/packages/seacas/Jamfile b/packages/seacas/Jamfile
@@ -1,9 +1,29 @@
 #---------------------------------------------------------------
-#    Copyright 2006, 2008 Sandia Corporation.
-#    Under the terms of Contract DE-AC04-94AL85000, there is a
-#    non-exclusive license for use of this work by or on behalf
-#    of the U.S. Government.  Export of this program may require
-#    a license from the United States Government.
+# Copyright (c) 2006--2017, National Technology & Engineering Solutions
+# of Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
+# NTESS, the U.S. Government retains certain rights in this software.
+# 
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#     * Redistributions of source code must retain the above copyright
+#       notice, this list of conditions and the following disclaimer.
+#     * Redistributions in binary form must reproduce the above copyright
+#       notice, this list of conditions and the following disclaimer in the
+#       documentation and/or other materials provided with the distribution.
+#     * Neither the name of NTESS nor the names of its contributors may
+#       be used to endorse or promote products derived from this
+#       software without specific prior written permission.
+# 
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
+# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #---------------------------------------------------------------
 
 #
@@ -99,6 +119,7 @@ alias install-targets
     Utst_superelement
     Utst_database_io
     Utst_sort
+    Utst_map
     $(seacas-root)/scripts/decomp
     /tpl/netcdf//nc_test
     /tpl/netcdf//ncdump
@@ -159,6 +180,7 @@ alias install-targets
     Utst_superelement
     Utst_database_io
     Utst_sort
+    Utst_map
     $(seacas-root)/scripts/blot
     $(seacas-root)/scripts/decomp
     $(seacas-root)/scripts/fastq
@@ -275,7 +297,6 @@ install install-user-lib
     ioinit
     ioss
     iotr
-    ioxf
     iovs
   : <target-os>bgq <location>$(install-root)/seacas/lib
   ;
@@ -306,7 +327,6 @@ install install-user-lib
     ioinit
     ioss
     iotr
-    ioxf
     iovs
   : <location>$(install-root)/seacas/lib
   ;
@@ -514,7 +534,6 @@ lib io_info_lib
     ioinit
     ioss
     iotr
-    ioxf
     iocgns
     /mpi//mpi
   : <define>USE_CGNS
@@ -660,26 +679,6 @@ lib iotr
     ]
   ;
 
-lib ioxf
-  :
-    [ ifdevbuild
-    # Any parameters within this 'ifdevbuild' block apply to development
-    # builds only and will not be present for user builds.
-        [ glob $(seacas-root)/libraries/ioss/src/xdmf/*.C ]
-    ]
-    ioss
-    /tpl/libxml2//xml
-    /tpl/xdmf//xdmf
-    /mpi//mpi
-  : 
-    [ ifuserbuild
-    # Any parameters within this 'ifuserbuild' block apply to user
-    # builds only and will not be present for developer builds.
-        <file>$(seacas-root)/lib/libioxf.a
-    ]
-  ;
-
-
 lib iovs
   :
     [ ifdevbuild
@@ -739,33 +738,30 @@ lib exodus
         [ glob $(seacas-root)/libraries/exodus/src/deprecated/*.c ]
     ]
     /tpl/netcdf//netcdf
-  :
+  : <define>EXODUS_IN_SIERRA
     [ ifdevbuild
     # Any parameters within this 'ifdevbuild' block apply to development
     # builds only and will not be present for user builds.
         <include>$(seacas-root)/libraries/exodus/include
         <include>$(seacas-root)/libraries/exodus/sierra
-	<define>PARALLEL_AWARE_EXODUS
     ]
     [ ifuserbuild
     # Any parameters within this 'ifuserbuild' block apply to user
     # builds only and will not be present for developer builds.
         <file>$(sierra-root)/seacas/lib/libexodus.a
     ]
   :
-  :
+  : <define>EXODUS_IN_SIERRA
     [ ifdevbuild
     # Any parameters within this 'ifdevbuild' block apply to development
     # builds only and will not be present for user builds.
         <include>$(seacas-root)/libraries/exodus/include
         <include>$(seacas-root)/libraries/exodus/sierra
-	<define>PARALLEL_AWARE_EXODUS
     ]
     [ ifuserbuild
     # Any parameters within this 'ifuserbuild' block apply to user
     # builds only and will not be present for developer builds.
         <include>$(sierra-root)/seacas/include/exodus
-	<define>PARALLEL_AWARE_EXODUS
     ]
   ;
 
@@ -1460,7 +1456,9 @@ lib aprepro_lib
             [ glob $(seacas-root)/libraries/aprepro_lib/apr_test.cc ]
         ]
     ]
-  :
+    exodus
+    /tpl/netcdf//netcdf
+  : <define>EXODUS_SUPPORT
     [ ifdevbuild
     # Any parameters within this 'ifdevbuild' block apply to development
     # builds only and will not be present for user builds.
@@ -1472,7 +1470,7 @@ lib aprepro_lib
         <file>$(sierra-root)/seacas/lib/libaprepro_lib.a
     ]
   :
-  :
+  : <define>EXODUS_SUPPORT
     [ ifdevbuild
     # Any parameters within this 'ifdevbuild' block apply to development
     # builds only and will not be present for user builds.
@@ -1824,7 +1822,6 @@ exe io_shell
     ioinit
     ioss
     iotr
-    ioxf
     /mpi//mpi
   : <define>USE_CGNS
     <tag>@sierra-exec-tag
@@ -1837,7 +1834,6 @@ exe io_info
     ioinit
     ioss
     iotr
-    ioxf
     /mpi//mpi
   : <define>USE_CGNS
     <tag>@sierra-exec-tag
@@ -1850,7 +1846,6 @@ exe shell_to_hex
     ioinit
     ioss
     iotr
-    ioxf
     /mpi//mpi
   : <tag>@sierra-exec-tag
   ;
@@ -1862,7 +1857,6 @@ exe cth_pressure_map
     ioinit
     ioss
     iotr
-    ioxf
     /mpi//mpi
   : <tag>@sierra-exec-tag
   ;
@@ -1873,7 +1867,6 @@ exe struc_to_unstruc
     ioinit
     ioss
     iotr
-    ioxf
     /mpi//mpi
   : <tag>@sierra-exec-tag
   ;
@@ -1894,6 +1887,14 @@ exe Utst_sort
   : <tag>@sierra-exec-tag
   ;
 
+exe Utst_map
+  :
+    $(seacas-root)/libraries/ioss/src/utest/Utst_map.C
+    ioss
+    /mpi//mpi
+  : <tag>@sierra-exec-tag
+  ;
+
 exe Utst_superelement
   :
     $(seacas-root)/libraries/ioss/src/utest/Utst_superelement.C

diff --git a/packages/seacas/NetCDF-Mapping.md b/packages/seacas/NetCDF-Mapping.md
@@ -1,5 +1,7 @@
 # Mapping of exodus entities onto NetCDF
 
+If you are using NetCDF-4.5.1 or later, then you can ignore the information in this file.
+
 The distributed version of netcdf sets the following limits
 on dimensions and variables:
  * `#define NC_MAX_DIMS	1024`

diff --git a/packages/seacas/README.md b/packages/seacas/README.md
@@ -17,6 +17,7 @@ build SEACAS
  * [Parallel-NetCDF](#parallel-netcdf) -- optional for parallel
  * [NetCDF](#netcdf) -- required with modifications
  * [MatIO](#matio) -- optional
+ * [DataWarehouse](#data_warehouse) -- optional
 
 #### Zoltan
 Zoltan is a package in Trilinos and it must be enabled for a SEACAS build.
@@ -63,15 +64,18 @@ support, you do not have to build hdf5.
 The most recent released version is recommended. For use with Exodus, some local modifications to the netcdf.h include file are required.  See [NetCDF-Mapping.md](NetCDF-Mapping.md) for an explanation of why these modifications are required (or highly recommended)
 
  * Download the latest netcdf-c release from http://www.unidata.ucar.edu/downloads/netcdf/index.jsp
- * `tar zxvf netcdf-4.4.0.tar.gz`  (or whatever the latest version is)
- * Modify the following defines in netcdf-4.4.0/include/netcdf.h.
+ * `tar zxvf netcdf-4.5.0.tar.gz`  (or whatever the latest version is)
+ * If the version is *prior* to 4.5.1, then you need to modify the
+   following defines in
+   seacas/TPL/netcdf/netcdf-4.5.0/include/netcdf.h.  Versions *4.5.1 or
+   later* do not check these limits and can be run unmodified.
 
     ```
     #define NC_MAX_DIMS     65536    /* max dimensions per file */
     #define NC_MAX_VARS     524288   /* max variables per file */
     ```
 
- * `cd netcdf-4.4.0` and enter the command:
+ * `cd netcdf-4.5.0` and enter the command:
     * serial
     ```
     CFLAGS="-I${WHERE_TO_INSTALL}/include" \
@@ -124,6 +128,27 @@ The MatIO library is used in the `exo2mat` and `mat2exo` programs which convert
 
  * `make && make install`
 
+#### DataWarehouse
+The Data Warehouse is a collection of data management tools that Sandia is currently developing to improve how datasets migrate between memory and storage resources in a distributed system. While the software is currently only available internally to Sandia, there will be an open source release of the tools during Fall of 2017. The Data Warehouse extensions to SEACAS are intended to serve as a placeholder for the upcoming release and are not intended for use by external developers at this time.
+
+The repository [data-warehouse-release](https://gitlab.sandia.gov/nessie-dev/data-warehouse-release) is a superbuild for the Data Warehouse tools and was created to make the build process as easy as possible. It includes the files INSTALL.md and INSTALL_TPL.md which contain instructions for building Data Warehouse and it's TPLs: Boost, googletest, libfabric, and libhio (optional). These builds are straightforward so a "runconfigure.sh" script is left to the end-user. Note that it's possible to supply your own build of these tools. Following the SEACAS pattern for building TPLs:
+
+
+    * cd TPL
+    * git clone git@gitlab.sandia.gov:nessie-dev/data-warehouse-release.git
+    * follow the instructions in INSTALL_TPL.md and then INSTALL.md
+    * consider installing data-warehouse-release and it's TPLs to the directory set in  the $ACCESS env. var.
+
+
+To build SEACAS with an installation of data-warehouse-release and it's TPLs, add the following lines to the list of cmake command arguments as found in the top-level _cmake-config_ file. Where DataWarehouse_PATH in environment variable that contains the path to the top-level install directory for the Data Warehouse, and HAVE_DATA_WAREHOUSE={ON|OFF} is a variable defined in _cmake-config_.
+
+
+    -DTPL_ENABLE_DATAWAREHOUSE:BOOL=${HAVE_DATAWAREHOUSE}           \
+    -DDataWarehouse_LIBRARY_DIRS:PATH=${DataWarehouse_PATH}/lib     \
+    -DDataWarehouse_INCLUDE_DIRS:PATH=${DataWarehouse_PATH}/include \
+
+
+
 ## Configure, Build, and Install Trilinos
 At this time, you should have all external TPL libraries built and
 installed into `${WHERE_TO_INSTALL}/lib` and `${WHERE_TO_INSTALL}/include`. You are now ready
@@ -158,5 +183,5 @@ There are a few unit tests for exodus, and aprepro that can be run via `make tes
 
 ## Contact information
 
- Greg Sjaardema  (gsjaardema@gmail.com, gdsjaar@sandia.gov)
+ Greg Sjaardema  (<gsjaardema@gmail.com>, <gdsjaar@sandia.gov>)
 
diff --git a/packages/seacas/applications/algebra/COPYRIGHT b/packages/seacas/applications/algebra/COPYRIGHT
@@ -1,4 +1,4 @@
-Copyright(C) 2008 National Technology & Engineering Solutions of
+Copyright(C) 2008-2017 National Technology & Engineering Solutions of
 Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
 NTESS, the U.S. Government retains certain rights in this software.
 

diff --git a/packages/seacas/applications/algebra/ag_addvar.f b/packages/seacas/applications/algebra/ag_addvar.f
@@ -1,4 +1,4 @@
-C    Copyright(C) 2008 National Technology & Engineering Solutions of
+C    Copyright(C) 2008-2017 National Technology & Engineering Solutions of
 C    Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
 C    NTESS, the U.S. Government retains certain rights in this software.
 C    

diff --git a/packages/seacas/applications/algebra/ag_alias.blk b/packages/seacas/applications/algebra/ag_alias.blk
@@ -1,4 +1,4 @@
-C    Copyright(C) 2008 National Technology & Engineering Solutions of
+C    Copyright(C) 2008-2017 National Technology & Engineering Solutions of
 C    Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
 C    NTESS, the U.S. Government retains certain rights in this software.
 C    

diff --git a/packages/seacas/applications/algebra/ag_alicmd.f b/packages/seacas/applications/algebra/ag_alicmd.f
@@ -1,4 +1,4 @@
-C    Copyright(C) 2008 National Technology & Engineering Solutions of
+C    Copyright(C) 2008-2017 National Technology & Engineering Solutions of
 C    Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
 C    NTESS, the U.S. Government retains certain rights in this software.
 C