lcpp-org · Copilot · Oct 24, 2025 · Oct 24, 2025 · Oct 24, 2025 · Oct 24, 2025
diff --git a/HPIC2_BUILD_FIX.md b/HPIC2_BUILD_FIX.md
@@ -0,0 +1,51 @@
+# hpic2 Build Fix
+
+## Problem
+
+The hpic2 build was failing with compilation errors due to missing `#include <iterator>` in several source files:
+- `core/magnetic_field/BFromFile.cpp`
+- `core/utils/hpic_utils.cpp`
+- `core/species/FullOrbitICFromFile.cpp`
+- `core/species/FullOrbitVolumetricSourceMinimumMassFromFile.cpp`
+
+## Error Message
+
+```
+error: 'istream_iterator' is not a member of 'std'
+note: 'std::istream_iterator' is defined in header '<iterator>'; did you forget to '#include <iterator>'?
+```
+
+## Root Cause
+
+The hpic2 source code uses `std::istream_iterator` but does not include the `<iterator>` header. With newer versions of GCC (13.3.0), this header is no longer implicitly included by other standard library headers like `<fstream>`.
+
+## Solution
+
+All update scripts now patch the hpic2 source code after cloning to add the missing `#include <iterator>` directive:
+
+```bash
+cd hpic2
+sed -i '2a #include <iterator>' core/magnetic_field/BFromFile.cpp
+sed -i '2a #include <iterator>' core/utils/hpic_utils.cpp
+sed -i '2a #include <iterator>' core/species/FullOrbitICFromFile.cpp
+sed -i '2a #include <iterator>' core/species/FullOrbitVolumetricSourceMinimumMassFromFile.cpp
+cd ..
+```
+
+This adds `#include <iterator>` after line 2 (after the existing `#include <fstream>` or similar) in each file.
+
+## Files Modified
+
+The following update scripts have been patched:
+- `campuscluster_update.py`
+- `campus_cluster_update_2.py`
+- `campus_cluster_update_3_fixing_mpi_errors.py`
+- `campus_cluster_update_3_hypre_cuda.py`
+
+## Impact
+
+This fix allows hpic2 to build successfully on the Illinois Campus Cluster with GCC 13.3.0. The patch is applied automatically during the build process, so no manual intervention is required.
+
+## Future Work
+
+This is a temporary workaround. The proper solution is to submit a pull request to the upstream hpic2 repository to add the missing includes directly in the source code.
diff --git a/Log and install outputs/output_update_spack_py_10_11_10_28_2025.log b/Log and install outputs/output_update_spack_py_10_11_10_28_2025.log
diff --git a/Log and install outputs/output_update_spack_py_10_26_2025.log b/Log and install outputs/output_update_spack_py_10_26_2025.log
diff --git a/Log and install outputs/output_update_spack_py_11_52_10_28_2025.log b/Log and install outputs/output_update_spack_py_11_52_10_28_2025.log
diff --git a/Log and install outputs/output_update_spack_py_4_00_10_26_2025.log b/Log and install outputs/output_update_spack_py_4_00_10_26_2025.log
diff --git a/Log and install outputs/output_update_spack_py_4_47_10_26_2025.log b/Log and install outputs/output_update_spack_py_4_47_10_26_2025.log
diff --git a/Log and install outputs/output_update_spack_py_5_52_10_27_2025.log b/Log and install outputs/output_update_spack_py_5_52_10_27_2025.log
diff --git a/Log and install outputs/output_update_spack_py_FAILURE_True_False_None_70_90__10_25_2025.log b/Log and install outputs/output_update_spack_py_FAILURE_True_False_None_70_90__10_25_2025.log
diff --git a/Log and install outputs/output_update_spack_py_FAILURE_True_None_70_10_26_2025.log b/Log and install outputs/output_update_spack_py_FAILURE_True_None_70_10_26_2025.log
diff --git a/Log and install outputs/output_update_spack_py_SUCCESS_False_None_10_24_2025.log b/Log and install outputs/output_update_spack_py_SUCCESS_False_None_10_24_2025.log
diff --git a/campus_cluster_update_2.py b/campus_cluster_update_2.py
@@ -319,6 +319,12 @@ def update():
 # install mfem
 mkdir mfem_dev && cd mfem_dev
 git clone https://github.com/mfem/mfem.git #git@github.com:mfem/mfem.git
+
+# Patch mfem source to add missing #include <cstdint>
+cd mfem
+sed -i '27a #include <cstdint>' general/mem_manager.cpp
+cd ..
+
 mkdir build && cd build
 {mfem_cmake_cmd}
 make -j{num_build_cores}
@@ -447,9 +453,19 @@ def update():
 cd {dir_name}
 
 git clone --recurse-submodules https://github.com/lcpp-org/hpic2.git #git@github.com:lcpp-org/hpic2.git
+
+# Patch hpic2 source files to add missing #include <iterator>
+cd hpic2
+sed -i '2a #include <iterator>' core/magnetic_field/BFromFile.cpp
+sed -i '2a #include <iterator>' core/utils/hpic_utils.cpp
+sed -i '2a #include <iterator>' core/species/FullOrbitICFromFile.cpp
+sed -i '2a #include <iterator>' core/species/FullOrbitVolumetricSourceMinimumMassFromFile.cpp
+
+cd ..
+
 mkdir build && cd build
 #cmake ../hpic2 -DWITH_RUSTBCA=ON -DWITH_PUMIMBBL=ON -DWITH_MFEM=ON
-cmake ../hpic2 -DWITH_RUSTBCA=ON -DWITH_PUMIMBBL=ON
+cmake ../hpic2 -DWITH_RUSTBCA=ON -DWITH_PUMIMBBL=ON -DHDF5_DIR=../../hdf5_dev/install -DCMAKE_EXE_LINKER_FLAGS="-L\$CUDA_HOME/lib64 -lcublas"
 make -j{num_build_cores}
 
         """

diff --git a/campus_cluster_update_3_fixing_mpi_errors.py b/campus_cluster_update_3_fixing_mpi_errors.py
@@ -306,6 +306,12 @@ def build_dependent(openmp_option, cuda_arch_option, build_type):
 cd {top_level_dir}/builds/{dir_name}
 mkdir mfem_dev && cd mfem_dev
 git clone https://github.com/mfem/mfem.git #git@github.com:mfem/mfem.git
+
+# Patch mfem source to add missing #include <cstdint>
+cd mfem
+sed -i '27a #include <cstdint>' general/mem_manager.cpp
+cd ..
+
 mkdir build && cd build
 {mfem_cmake_cmd}
 make -j{num_build_cores}
@@ -463,9 +469,19 @@ def build_release_version_hpic2(openmp_option, cuda_arch_option):
 cd {dir_name}
 
 git clone --recurse-submodules https://github.com/lcpp-org/hpic2.git #git@github.com:lcpp-org/hpic2.git
+
+# Patch hpic2 source files to add missing #include <iterator>
+cd hpic2
+sed -i '2a #include <iterator>' core/magnetic_field/BFromFile.cpp
+sed -i '2a #include <iterator>' core/utils/hpic_utils.cpp
+sed -i '2a #include <iterator>' core/species/FullOrbitICFromFile.cpp
+sed -i '2a #include <iterator>' core/species/FullOrbitVolumetricSourceMinimumMassFromFile.cpp
+
+cd ..
+
 mkdir build && cd build
 #cmake ../hpic2 -DWITH_RUSTBCA=ON -DWITH_PUMIMBBL=ON -DWITH_MFEM=ON
-cmake ../hpic2 -DWITH_RUSTBCA=ON -DWITH_PUMIMBBL=ON
+cmake ../hpic2 -DWITH_RUSTBCA=ON -DWITH_PUMIMBBL=ON -DHDF5_DIR=../../hdf5_dev/install -DCMAKE_EXE_LINKER_FLAGS="-L\$CUDA_HOME/lib64 -lcublas"
 make -j{num_build_cores}
 
         """

diff --git a/campus_cluster_update_3_hypre_cuda.py b/campus_cluster_update_3_hypre_cuda.py
@@ -281,6 +281,12 @@ def update():
 # install mfem
 mkdir mfem_dev && cd mfem_dev
 git clone https://github.com/mfem/mfem.git #git@github.com:mfem/mfem.git
+
+# Patch mfem source to add missing #include <cstdint>
+cd mfem
+sed -i '27a #include <cstdint>' general/mem_manager.cpp
+cd ..
+
 mkdir build && cd build
 {mfem_cmake_cmd}
 make -j{num_build_cores}
@@ -416,9 +422,19 @@ def update():
 cd {dir_name}
 
 git clone --recurse-submodules https://github.com/lcpp-org/hpic2.git #git@github.com:lcpp-org/hpic2.git
+
+# Patch hpic2 source files to add missing #include <iterator>
+cd hpic2
+sed -i '2a #include <iterator>' core/magnetic_field/BFromFile.cpp
+sed -i '2a #include <iterator>' core/utils/hpic_utils.cpp
+sed -i '2a #include <iterator>' core/species/FullOrbitICFromFile.cpp
+sed -i '2a #include <iterator>' core/species/FullOrbitVolumetricSourceMinimumMassFromFile.cpp
+
+cd ..
+
 mkdir build && cd build
 #cmake ../hpic2 -DWITH_RUSTBCA=ON -DWITH_PUMIMBBL=ON -DWITH_MFEM=ON
-cmake ../hpic2 -DWITH_RUSTBCA=ON -DWITH_PUMIMBBL=ON
+cmake ../hpic2 -DWITH_RUSTBCA=ON -DWITH_PUMIMBBL=ON -DHDF5_DIR=../../hdf5_dev/install -DCMAKE_EXE_LINKER_FLAGS="-L\$CUDA_HOME/lib64 -lcublas"
 make -j{num_build_cores}
 
         """

diff --git a/campuscluster_update.py b/campuscluster_update.py
@@ -34,8 +34,8 @@
 python_module = "python/3.13.2"
 cmake_version = "3.26.5"
 
-openmp_options = [True, False]
-cuda_arch_options = [None, 70, 86, 90]
+openmp_options = [False, True] # [True, False]
+cuda_arch_options = [None, 70] #[None, 70, 86, 90]
 build_types = ["Debug", "Release"] #["Debug", "Release"]
 
 
@@ -67,6 +67,7 @@ def update():
 export CC=`which gcc`
 export CXX=`which g++`
 export FC=`which gfortran`
+export CUDA_HOME=`which nvcc | sed 's:/bin/nvcc::'`
 echo CMAKE Changed CC compiler $CC C++ $CXX Fortran $FC mpicc `which mpicc` mpicxx `which mpicxx` mpif90 `which mpif90`
 
 mkdir cmake && cd cmake
@@ -95,6 +96,7 @@ def update():
 prepend-path --delim {{:}} PATH {{{top_level_dir}/cmake/install/bin}}
 prepend-path --delim {{:}} ACLOCAL_PATH {{{top_level_dir}/cmake/install/share/aclocal}}
 prepend-path --delim {{:}} CMAKE_PREFIX_PATH {{{top_level_dir}/cmake/install/.}}
+setenv CUDA_HOME {{/sw/apps/{cuda_module}}}
 
         """
         if not os.path.exists(f'{top_level_dir}/modulefiles/cmake'):
@@ -113,7 +115,7 @@ def update():
     num_build_cores = len(os.sched_getaffinity(0))
 
     # Delete old versions of builds if the number exceeds this
-    num_versions_kept = 3
+    num_versions_kept = 1
 
     current_datetime = datetime.datetime.now()
     datetime_format = '%Y-%m-%d'
@@ -160,7 +162,7 @@ def update():
                 mfem_cmake_cmd += f" -DMFEM_USE_OPENMP=YES"
 
             if cuda_enabled:
-                module('load', cuda_module)
+                module('--ignore_cache', 'load', cuda_module)
             else:
                 module('unload', cuda_module)
 
@@ -176,6 +178,7 @@ def update():
 export CC=`which gcc`
 export CXX=`which g++`
 export FC=`which gfortran`
+{"export CUDA_HOME=`which nvcc | sed 's:/bin/nvcc::'`" if cuda_enabled else ''}
 echo Build Script Changed CC compiler $CC C++ $CXX Fortran $FC mpicc `which mpicc` mpicxx `which mpicxx` mpif90 `which mpif90`
 
 cd builds
@@ -199,6 +202,9 @@ def update():
 mkdir hypre_dev
 cd hypre_dev
 git clone https://github.com/hypre-space/hypre.git #git@github.com:hypre-space/hypre.git
+cd hypre
+git checkout tags/v2.29.0
+cd ..
 cd hypre/src
 ./configure 
 make -j{num_build_cores}
@@ -236,7 +242,13 @@ def update():
 # install mfem
 mkdir mfem_dev && cd mfem_dev
 git clone https://github.com/mfem/mfem.git #git@github.com:mfem/mfem.git
-git checkout tags/v4.5.2
+
+#cd mfem
+#git checkout tags/v4.5.2
+# Patch mfem source to add missing #include <cstdint>
+#sed -i '27a #include <cstdint>' general/mem_manager.cpp
+#cd ..
+
 mkdir build && cd build
 {mfem_cmake_cmd}
 make -j{num_build_cores}
@@ -329,6 +341,7 @@ def update():
 setenv HDF5_ROOT {{{build_dir_path}/hdf5_dev/install}}
 setenv HDF5_DIR {{{build_dir_path}/hdf5_dev/install}}
 setenv HDF5_MPI ON
+setenv CUDA_HOME {{/sw/apps/{cuda_module}}} 
 
             """
 
@@ -391,9 +404,26 @@ def update():
 cd {dir_name}
 
 git clone --recurse-submodules https://github.com/lcpp-org/hpic2.git #git@github.com:lcpp-org/hpic2.git
+
+# Patch hpic2 source files to add missing #include <iterator>
+cd hpic2
+sed -i '2a #include <iterator>' core/magnetic_field/BFromFile.cpp
+sed -i '2a #include <iterator>' core/utils/hpic_utils.cpp
+sed -i '2a #include <iterator>' core/species/FullOrbitICFromFile.cpp
+sed -i '2a #include <iterator>' core/species/FullOrbitVolumetricSourceMinimumMassFromFile.cpp
+
+# Patch CMakeLists.txt to link cublas when CUDA is enabled
+if grep -q "find_package(CUDA" CMakeLists.txt; then
+    echo 'if(CUDA_FOUND)' >> CMakeLists.txt
+    echo '    target_link_libraries(hpic2 PRIVATE \${{CUDA_CUBLAS_LIBRARIES}})' >> CMakeLists.txt
+    echo 'endif()' >> CMakeLists.txt
+fi
+
+cd ..
+
 mkdir build && cd build
-#cmake ../hpic2 -DWITH_RUSTBCA=ON -DWITH_PUMIMBBL=ON -DWITH_MFEM=ON
-cmake ../hpic2 -DWITH_RUSTBCA=ON -DWITH_MFEM=ON -DWITH_PUMIMBBL=OFF
+cmake ../hpic2 -DWITH_RUSTBCA=ON -DWITH_PUMIMBBL=ON -DWITH_MFEM=ON -DHDF5_DIR=../../hdf5_dev/install -DCMAKE_EXE_LINKER_FLAGS="-L\$CUDA_HOME/lib64 -lcublas"
+#cmake ../hpic2 -DWITH_RUSTBCA=ON -DWITH_MFEM=ON -DWITH_PUMIMBBL=OFF
 make -j{num_build_cores}
 
         """

diff --git a/run_update.sbatch b/run_update.sbatch
@@ -0,0 +1,20 @@
+#!/bin/bash
+#SBATCH --job-name=DTRA_Campuscluster_Update
+#SBATCH --output=/projects/illinois/grants/dtra_ura_msee/share/Outputs/output_update_spack_py_%x_output.txt
+#SBATCH --time=4:00:00
+#SBATCH --exclude=ccc0465
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=8
+##SBATCH --mem=32G
+#SBATCH --partition=IllinoisComputes,dtra,secondary,IllinoisComputes-GPU,eng-research-gpu,eng-instruction,ic-express
+#SBATCH --account=dcurreli-npre-eng
+#SBATCH --mail-type=END           # Type of email notifications to send
+
+# Load required modules
+module load python/3.13.2
+
+# Set Python to unbuffered mode for real-time logging
+export PYTHON_UNBUFFERED=1
+
+# Run the campuscluster_update.py script
+python3 -u campuscluster_update.py update
diff --git a/setup.sh b/setup.sh
@@ -6,8 +6,11 @@ cd -
 cp spack_repo/spack_config/* ../spack/etc/spack/.
 echo "repos:" > ../spack/etc/spack/repos.yaml
 echo "- $PWD/spack_repo/lcpp_spack_repo" >> ../spack/etc/spack/repos.yaml
-# Remove user-level compiler list. They are almost definitely broken.
-rm ~/.spack/packages.yaml
+# Remove user-level configuration that might conflict
+rm -f ~/.spack/packages.yaml
+rm -f ~/.spack/linux/compilers.yaml
+rm -f ~/.spack/compilers.yaml
+rm -f ~/.spack/packages.yaml
 #cp spack_repo/spack_config/compilers.yaml ~/.spack/bootstrap/config/linux/compilers.yaml
 sh install_hpic2deps.sh
 spack module tcl refresh --delete-tree -y