Automatic snapshot commit from seacas at 94e88d4519

Origin repo remote tracking branch: 'origin/master' Origin repo remote repo URL: 'origin = https://github.com/sandialabs/seacas' Git describe: i2024-11-15-47-gc376c98dfe At commit: commit 94e88d451990cea8ff5520c769e6d29e0fd7cb9d Author: Greg Sjaardema <[email protected]> Date: Tue Jan 28 15:58:59 2025 -0700 Summary: IOSS: cgns - minor tweak to decomposition algorithm to avoid 0 intervals * Several files -- remove trailing whitespace * Several -- Cleanups from compiler and static analyzer warnings * Exodiff -- Use Namelist as alias for std::vector<std::string>, Rename class ExoII_Read to Exo_Read * Aprepro -- better error detection/reporting. Support string+string for concatenation in addition to // * Aprepro -- add a `format` function to print variable using a specified output format. * Exodus -- clean up lots of trailing whitespace in tests * Exodus -- support additional compression algorithms * IOSS -- New change-set (dynamic topology) code [Tolu primarily] * IOSS -- cgns decomp - fix bug giving 0 intervals on a zone * nem_slice -- Use enum class and rename some enums * Compression -- add zstd, bz2, and lossy quantize compression to several apps Signed-off-by: Greg Sjaardema <[email protected]>
trilinos · Jan 29, 2025 · 0a5f02f · 0a5f02f
1 parent 15038f6
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diff --git a/packages/seacas/Jamfile b/packages/seacas/Jamfile
@@ -168,7 +168,7 @@ explicit install-user-include0 ;
 install install-user-include0
   : [ glob $(seacas-root)/libraries/ioss/src/*.h
            $(seacas-root)/libraries/ioss/src/init/*.h ]
-  : <location>$(install-root)/io_system/include
+  : <location>$(install-root)/Sierra/include/io_system
   ;
 
 explicit install-user-include1 ;
@@ -222,7 +222,7 @@ install install-user-include6
   : [ glob $(seacas-root)/libraries/ioss/src/visualization/utils/*.h
            $(seacas-root)/libraries/ioss/src/visualization/exodus/*.h
            $(seacas-root)/libraries/ioss/src/visualization/cgns/*.h ]
-  : <location>$(install-root)/io_system/include
+  : <location>$(install-root)/Sierra/include/io_system
   ;
 
 

diff --git a/packages/seacas/applications/aprepro/test.inp_app b/packages/seacas/applications/aprepro/test.inp_app
@@ -180,7 +180,7 @@ $ Test int and [] (shortcut for int)
 
 $ Test looping - print sin, cos from 0 to 90 by 5
 {Loop(19, _angle, 0, 5)}
-{_angle}	{_sa=sind(_angle)}	{_ca=cosd(_angle)} {hypot(_sa, _ca)} 
+{_angle}	{_sa=sind(_angle)}	{_ca=cosd(_angle)} {hypot(_sa, _ca)}
 {EndLoop}
 
 $$$$ Test formatting and string concatenation
@@ -200,12 +200,12 @@ $$$$ Test string rescanning and executing
 Original String:
 {Test}
 Rescanned String:
-{rescan(Test)} 
+{rescan(Test)}
 Original String:
 {Test2}
 Print Value of variable T = {T}
 Rescanned String:
-{rescan(Test2)} 
+{rescan(Test2)}
 Print Value of variable T = {T}
 
 Original String: {t1 = "atan2(0,-1)"}

diff --git a/packages/seacas/applications/aprepro/test_standard.out b/packages/seacas/applications/aprepro/test_standard.out
@@ -3,7 +3,7 @@ $
 Test number representations
 1	1	1	1	1
 1	1	1	1	1
-	
+
 Test assign statements:
 5	5	$ Should print 5 5
 10	10 	$ Should print 10 10
@@ -51,8 +51,8 @@ $ Test ifndef - else lines
  This line should be echoed (6)
     This line should be echoed. (7)
 $ Lines a, b, c, d, 1, 4, 6, 7 should be echoed
-$ Check line counting -- should be on line 78: 
- 
+$ Check line counting -- should be on line 78:
+
 $ ========================================================================
 $ Test string if lines
  This line should be echoed ("greg")
@@ -89,25 +89,25 @@ $ Test int and [] (shortcut for int)
 5	-5
 
 $ Test looping - print sin, cos from 0 to 90 by 5
-0	0	1 1 
-5	0.08715574275	0.9961946981 1 
-10	0.1736481777	0.984807753 1 
-15	0.2588190451	0.9659258263 1 
-20	0.3420201433	0.9396926208 1 
-25	0.4226182617	0.906307787 1 
-30	0.5	0.8660254038 1 
-35	0.5735764364	0.8191520443 1 
-40	0.6427876097	0.7660444431 1 
-45	0.7071067812	0.7071067812 1 
-50	0.7660444431	0.6427876097 1 
-55	0.8191520443	0.5735764364 1 
-60	0.8660254038	0.5 1 
-65	0.906307787	0.4226182617 1 
-70	0.9396926208	0.3420201433 1 
-75	0.9659258263	0.2588190451 1 
-80	0.984807753	0.1736481777 1 
-85	0.9961946981	0.08715574275 1 
-90	1	6.123233996e-17 1 
+0	0	1 1
+5	0.08715574275	0.9961946981 1
+10	0.1736481777	0.984807753 1
+15	0.2588190451	0.9659258263 1
+20	0.3420201433	0.9396926208 1
+25	0.4226182617	0.906307787 1
+30	0.5	0.8660254038 1
+35	0.5735764364	0.8191520443 1
+40	0.6427876097	0.7660444431 1
+45	0.7071067812	0.7071067812 1
+50	0.7660444431	0.6427876097 1
+55	0.8191520443	0.5735764364 1
+60	0.8660254038	0.5 1
+65	0.906307787	0.4226182617 1
+70	0.9396926208	0.3420201433 1
+75	0.9659258263	0.2588190451 1
+80	0.984807753	0.1736481777 1
+85	0.9961946981	0.08715574275 1
+90	1	6.123233996e-17 1
 
 $$$$ Test formatting and string concatenation
 %.10g
@@ -142,12 +142,12 @@ Original String:
 Rescanned String:
 	This is line 1: 3.141592654
         This is line 2: 0.7071067812
-	This is line 3: 0.7071067812 
+	This is line 3: 0.7071067812
 Original String:
 This has an embedded string: {T = "This is a string"}
 Print Value of variable T = 0
 Rescanned String:
-This has an embedded string: This is a string 
+This has an embedded string: This is a string
 Print Value of variable T = This is a string
 
 Original String: atan2(0,-1)

diff --git a/packages/seacas/applications/blot/grpcom.blk b/packages/seacas/applications/blot/grpcom.blk
@@ -1,4 +1,4 @@
-C    Copyright(C) 1999-2020 National Technology & Engineering Solutions
+C    Copyright(C) 1999-2020, 2024 National Technology & Engineering Solutions
 C    of Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
 C    NTESS, the U.S. Government retains certain rights in this software.
 C
@@ -7,7 +7,7 @@ C    See packages/seacas/LICENSE for details
       COMMON /GRPCOC/ DEVNAM(2), DEVCOD(2)
       CHARACTER*3 DEVNAM
       CHARACTER*8 DEVCOD
-      COMMON /GRPCOM/ ICURDV, 
+      COMMON /GRPCOM/ ICURDV,
      &   NSNAP(2), IFONT(2),
      &   MAXCOL(2), NUMCOL(0:1,2), MAPALT(2), MAPUSE(2),
      &   ISHARD, DEVOK(2), TALKOK(2), SOFTCH(2), AUTOPL(2)

diff --git a/packages/seacas/applications/blot/mshcol.f b/packages/seacas/applications/blot/mshcol.f
@@ -1,4 +1,4 @@
-C Copyright(C) 1999-2020 National Technology & Engineering Solutions
+C Copyright(C) 1999-2020, 2024 National Technology & Engineering Solutions
 C of Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
 C NTESS, the U.S. Government retains certain rights in this software.
 C
@@ -53,7 +53,7 @@ SUBROUTINE MSHCOL (FNCT, IELB, MLNTYP, WIDLIN, BLKCOL,
 
       include 'dbnums.blk'
       include 'linthc.blk'
-      
+
       CHARACTER*(*) FNCT
       INTEGER MLNTYP(-1:1)
       LOGICAL WIDLIN

diff --git a/packages/seacas/applications/conjoin/CJ_ExodusFile.C b/packages/seacas/applications/conjoin/CJ_ExodusFile.C
@@ -1,4 +1,4 @@
-// Copyright(C) 1999-2021, 2023 National Technology & Engineering Solutions
+// Copyright(C) 1999-2021, 2023, 2024 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.
 //
@@ -202,6 +202,16 @@ bool Excn::ExodusFile::create_output(const SystemInterface &si)
     else if (si.zlib()) {
       ex_set_option(outputId_, EX_OPT_COMPRESSION_TYPE, EX_COMPRESS_ZLIB);
     }
+    else if (si.zstd()) {
+      ex_set_option(outputId_, EX_OPT_COMPRESSION_TYPE, EX_COMPRESS_ZSTD);
+    }
+    else if (si.bz2()) {
+      ex_set_option(outputId_, EX_OPT_COMPRESSION_TYPE, EX_COMPRESS_BZ2);
+    }
+
+    if (si.quantize()) {
+      ex_set_option(outputId_, EX_OPT_QUANTIZE_NSD, si.quantize_nsd());
+    }
   }
 
   fmt::print("IO Word size is {} bytes.\n", ioWordSize_);

diff --git a/packages/seacas/applications/conjoin/CJ_SystemInterface.C b/packages/seacas/applications/conjoin/CJ_SystemInterface.C
@@ -65,18 +65,27 @@ void Excn::SystemInterface::enroll_options()
   options_.enroll("64-bit", GetLongOption::NoValue,
                   "True if forcing the use of 64-bit integers for the output file", nullptr);
 
-  options_.enroll(
-      "zlib", GetLongOption::NoValue,
-      "Use the Zlib / libz compression method if compression is enabled (default) [exodus only].",
-      nullptr);
+  options_.enroll("zlib", GetLongOption::NoValue,
+                  "Use the Zlib / libz compression method if compression is enabled (default) "
+                  "[exodus only, enables netcdf-4].",
+                  nullptr);
 
   options_.enroll("szip", GetLongOption::NoValue,
                   "Use SZip compression. [exodus only, enables netcdf-4]", nullptr);
+  options_.enroll("zstd", GetLongOption::NoValue,
+                  "Use Zstd compression. [exodus only, enables netcdf-4, experimental]", nullptr);
+  options_.enroll("bzip2", GetLongOption::NoValue,
+                  "Use Bzip2 compression. [exodus only, enables netcdf-4, experimental]", nullptr);
+
+  options_.enroll("compress", GetLongOption::MandatoryValue,
+                  "Specify the compression level to be used.  Values depend on algorithm:\n"
+                  "\t\tzlib/bzip2:  0..9\t\tszip:  even, 4..32\t\tzstd:  -131072..22",
+                  nullptr);
 
-  options_.enroll(
-      "compress", GetLongOption::MandatoryValue,
-      "Specify the hdf5 (netcdf4) compression level [0..9] to be used on the output file.", nullptr,
-      nullptr, true);
+  options_.enroll("quantize_nsd", GetLongOption::MandatoryValue,
+                  "Use the lossy quantize compression method.  Value specifies number of digits to "
+                  "retain (1..15) [exodus only]",
+                  nullptr, nullptr, true);
 
   options_.enroll("sort_times", GetLongOption::NoValue,
                   "Sort the input files on the minimum timestep time in the file.\n"
@@ -242,17 +251,61 @@ bool Excn::SystemInterface::parse_options(int argc, char **argv)
   omitNodesets_      = options_.retrieve("omit_nodesets") != nullptr;
   omitSidesets_      = options_.retrieve("omit_sidesets") != nullptr;
 
-  if (options_.retrieve("szip") != nullptr) {
-    szip_ = true;
-    zlib_ = false;
-  }
   zlib_ = (options_.retrieve("zlib") != nullptr);
+  szip_ = (options_.retrieve("szip") != nullptr);
+  zstd_ = (options_.retrieve("zstd") != nullptr);
+  bz2_  = (options_.retrieve("bzip2") != nullptr);
+
+  if (szip_ + zlib_ + zstd_ + bz2_ > 1) {
+    fmt::print(stderr,
+               "ERROR: Only one of 'szip' or 'zlib' or 'zstd' or 'bzip2' can be specified.\n");
+  }
+
+  {
+    const char *temp = options_.retrieve("compress");
+    if (temp != nullptr) {
+      compressionLevel_ = std::strtol(temp, nullptr, 10);
+      if (!szip_ && !zlib_ && !zstd_ && !bz2_) {
+        zlib_ = true;
+      }
 
-  if (szip_ && zlib_) {
-    fmt::print(stderr, "ERROR: Only one of 'szip' or 'zlib' can be specified.\n");
+      if (zlib_ || bz2_) {
+        if (compressionLevel_ < 0 || compressionLevel_ > 9) {
+          fmt::print(stderr,
+                     "ERROR: Bad compression level {}, valid value is between 0 and 9 inclusive "
+                     "for gzip/zlib/bzip2 compression.\n",
+                     compressionLevel_);
+          return false;
+        }
+      }
+      else if (szip_) {
+        if (compressionLevel_ % 2 != 0) {
+          fmt::print(
+              stderr,
+              "ERROR: Bad compression level {}. Must be an even value for szip compression.\n",
+              compressionLevel_);
+          return false;
+        }
+        if (compressionLevel_ < 4 || compressionLevel_ > 32) {
+          fmt::print(stderr,
+                     "ERROR: Bad compression level {}, valid value is between 4 and 32 inclusive "
+                     "for szip compression.\n",
+                     compressionLevel_);
+          return false;
+        }
+      }
+    }
   }
 
-  compressionLevel_ = options_.get_option_value("compress", compressionLevel_);
+  {
+    const char *temp = options_.retrieve("quantize_nsd");
+    if (temp != nullptr) {
+      quantizeNSD_ = std::strtol(temp, nullptr, 10);
+      if (!szip_ && !zlib_ && !zstd_ && !bz2_) {
+        zlib_ = true;
+      }
+    }
+  }
 
   if (options_.retrieve("copyright") != nullptr) {
     fmt::print("{}", copyright("2009-2021"));

diff --git a/packages/seacas/applications/conjoin/CJ_SystemInterface.h b/packages/seacas/applications/conjoin/CJ_SystemInterface.h
@@ -17,11 +17,16 @@ namespace Excn {
     SystemInterface();
     bool parse_options(int argc, char **argv);
 
-    int  debug() const { return debugLevel_; }
-    int  screen_width() const { return screenWidth_; }
+    int debug() const { return debugLevel_; }
+    int screen_width() const { return screenWidth_; }
+
+    int  quantize_nsd() const { return quantizeNSD_; }
     int  compress_data() const { return compressionLevel_; }
     bool zlib() const { return zlib_; }
     bool szip() const { return szip_; }
+    bool zstd() const { return zstd_; }
+    bool bz2() const { return bz2_; }
+    bool quantize() const { return quantizeNSD_ > 0; }
 
     bool omit_nodesets() const { return omitNodesets_; }
     bool omit_sidesets() const { return omitSidesets_; }
@@ -60,8 +65,11 @@ namespace Excn {
     int  debugLevel_{0};
     int  screenWidth_{0};
     int  compressionLevel_{0};
-    bool zlib_{true};
+    int  quantizeNSD_{0};
+    bool zlib_{false};
     bool szip_{false};
+    bool zstd_{false};
+    bool bz2_{false};
     bool omitNodesets_{false};
     bool omitSidesets_{false};
     bool ints64Bit_{false};

diff --git a/packages/seacas/applications/conjoin/Conjoin.C b/packages/seacas/applications/conjoin/Conjoin.C
@@ -1535,6 +1535,9 @@ namespace {
 
     global->elementCount = goffset;
     global_element_map.resize(goffset);
+    if (goffset == 0) {
+      return;
+    }
 
     size_t max_id        = global_element_map[global->elementCount - 1].first;
     bool   is_contiguous = max_id == global_element_map.size();
@@ -2203,7 +2206,7 @@ namespace {
       for (size_t ns = 0; ns < set_ids.size(); ns++) {
 
         std::vector<INT> glob_ns_nodes(total_node_count + 1);
-        std::fill(glob_ns_nodes.begin(), glob_ns_nodes.end(), 0);
+        std::fill(glob_ns_nodes.begin(), glob_ns_nodes.end(), (INT)0);
 
         size_t lns = glob_sets[ns].position_;
         for (size_t p = 0; p < part_count; p++) {
@@ -2548,7 +2551,7 @@ namespace {
 
     for (size_t b = 0; b < global.count(Excn::ObjectType::EBLK); b++) {
       status.resize(glob_blocks[b].entity_count());
-      std::fill(status.begin(), status.end(), (1.0 - alive));
+      std::fill(status.begin(), status.end(), T(1.0 - alive));
       size_t boffset       = blocks[b].offset_;
       size_t goffset       = glob_blocks[b].offset_;
       size_t element_count = blocks[b].entity_count();

diff --git a/packages/seacas/applications/cpup/CP_SystemInterface.C b/packages/seacas/applications/cpup/CP_SystemInterface.C
@@ -124,19 +124,6 @@ void Cpup::SystemInterface::enroll_options()
       "large subcycle runs.",
       nullptr);
 
-  options_.enroll(
-      "zlib", GetLongOption::NoValue,
-      "Use the Zlib / libz compression method if compression is enabled (default) [exodus only].",
-      nullptr);
-
-  options_.enroll("szip", GetLongOption::NoValue,
-                  "Use SZip compression. [exodus only, enables netcdf-4]", nullptr);
-
-  options_.enroll("compress_data", GetLongOption::MandatoryValue,
-                  "The output database will be written using compression (netcdf-4 mode only).\n"
-                  "\t\tValue ranges from 0..9 for zlib/gzip or even values 4..32 for szip.",
-                  nullptr, nullptr, true);
-
   options_.enroll("append", GetLongOption::NoValue,
                   "Append to database instead of opening a new database.\n"
                   "\t\tTimestep transfer will start after last timestep on database",
@@ -301,18 +288,7 @@ bool Cpup::SystemInterface::parse_options(int argc, char **argv)
 
   append_ = options_.retrieve("append") != nullptr;
 
-  if (options_.retrieve("szip") != nullptr) {
-    szip_ = true;
-    zlib_ = false;
-  }
-  zlib_ = (options_.retrieve("zlib") != nullptr);
-
-  if (szip_ && zlib_) {
-    fmt::print(stderr, "ERROR: Only one of 'szip' or 'zlib' can be specified.\n");
-  }
-
   append_ = options_.retrieve("append") != nullptr;
-  compressData_ = options_.get_option_value("compress_data", compressData_);
   //subcycle_        = options_.get_option_value("subcycle", subcycle_);
   cycle_           = options_.get_option_value("cycle", cycle_);
   subcycleJoin_    = options_.retrieve("join_subcycles") != nullptr;

diff --git a/packages/seacas/applications/cpup/CP_SystemInterface.h b/packages/seacas/applications/cpup/CP_SystemInterface.h
@@ -65,9 +65,6 @@ namespace Cpup {
     bool map_element_ids() const { return mapIds_; }
     bool omit_nodesets() const { return omitNodesets_; }
     bool omit_sidesets() const { return omitSidesets_; }
-    int  compress_data() const { return compressData_; }
-    bool zlib() const { return zlib_; }
-    bool szip() const { return szip_; }
     bool subcycle_join() const { return subcycleJoin_; }
     bool keep_temporary() const { return keepTemporary_; }
     bool verify_valid_file() const { return verifyValidFile_; }
@@ -132,10 +129,7 @@ namespace Cpup {
     int  partCount_{-1};
     int  subcycle_{-1};
     int  cycle_{-1};
-    int  compressData_{0};
     int  maxOpenFiles_{0};
-    bool zlib_{true};
-    bool szip_{false};
     bool sumSharedNodes_{false};
     bool addProcessorIdField_{false};
     bool addProcessorIdMap_{false};