From d67ad053ed34c623dc0213b67398ad7a0ba537d7 Mon Sep 17 00:00:00 2001
From: arnav-singhal <43693924+arnav-singhal@users.noreply.github.com>
Date: Fri, 19 Jul 2024 18:46:06 -0700
Subject: [PATCH] Make HDF5 optional (#64)

* make hdf5 optional

* mention conda env
---
 CMakeLists.txt |  1 -
 README.md      | 14 ++++++++++++--
 src/IO.cpp     | 18 ++++++++++++++++++
 3 files changed, 30 insertions(+), 3 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 1645e9f..216026c 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -15,7 +15,6 @@ set(AMReX_TINY_PROFILE    ON)
 set(AMReX_SPACEDIM 2 CACHE INTERNAL "")
 set(AMReX_PRECISION SINGLE CACHE INTERNAL "")
 set(AMReX_PARTICLES_PRECISION SINGLE CACHE INTERNAL "")
-set(AMReX_HDF5          TRUE)
 
 #
 # Fetch amrex repo
diff --git a/README.md b/README.md
index 89457cc..45ba264 100644
--- a/README.md
+++ b/README.md
@@ -15,8 +15,18 @@ This demo uses CMake version 3.14 or higher. To build it:
 
 To build with GPU support, use the `-DAMReX_GPU_BACKEND=CUDA` CMake option.
 
-For convenience, a script for setting up the module environment for Perlmutter is
-provided in etc/perlmutter_environment.sh. To use it, do:
+To write output as (compressed) HDF5, use the `-DAMReX_HDF5=TRUE` CMake option.
+Parallel HDF5 installation is required. On perlmutter, a conda environment is
+available at:
+
+    conda activate /global/common/software/m3623/exaepi
+
+Compression level can be altered in src/IO.cpp file. The environment variable
+HDF5_CHUNK_SIZE controls the chunk size if compression is used. A value of 
+around 100,000 is recommended to start.
+
+For convenience, a script for setting up the module environment without HDF5
+for Perlmutter is provided in etc/perlmutter_environment.sh. To use it, do:
 
     source etc/perlmutter_environment.sh
 
diff --git a/src/IO.cpp b/src/IO.cpp
index 4558d3d..5ffba02 100644
--- a/src/IO.cpp
+++ b/src/IO.cpp
@@ -88,6 +88,7 @@ void writePlotFile (const AgentContainer& pc, /*!< Agent (particle) container */
         plt_varnames.push_back("Tract");
         plt_varnames.push_back("comm");
 
+#ifdef AMREX_USE_HDF5
         WriteSingleLevelPlotfileHDF5MultiDset(  amrex::Concatenate("plt", step, 5),
                                                 output_mf,
                                                 plt_varnames,
@@ -95,6 +96,14 @@ void writePlotFile (const AgentContainer& pc, /*!< Agent (particle) container */
                                                 cur_time,
                                                 step,
                                                 "ZLIB@3" );
+#else
+        WriteSingleLevelPlotfile(   amrex::Concatenate("plt", step, 5),
+                                    output_mf,
+                                    plt_varnames,
+                                    pc.ParticleGeom(0),
+                                    cur_time,
+                                    step );
+#endif
     }
 
     {
@@ -136,6 +145,7 @@ void writePlotFile (const AgentContainer& pc, /*!< Agent (particle) container */
             }
         }
 
+#ifdef AMREX_USE_HDF5
         pc.WritePlotFileHDF5(   amrex::Concatenate("plt", step, 5),
                                 "agents",
                                 write_real_comp,
@@ -143,6 +153,14 @@ void writePlotFile (const AgentContainer& pc, /*!< Agent (particle) container */
                                 real_varnames,
                                 int_varnames,
                                 "ZLIB@3" );
+#else
+        pc.WritePlotFile(   amrex::Concatenate("plt", step, 5),
+                            "agents",
+                            write_real_comp,
+                            write_int_comp,
+                            real_varnames,
+                            int_varnames );
+#endif
     }
 }