Remove flex/bison from dockerfiles, should install correct versions via spack

klevzoff · klevzoff · commit 3046faf49372 · 2025-08-08T09:44:15.000-07:00
diff --git a/docker/Stanford/Dockerfile b/docker/Stanford/Dockerfile
@@ -49,8 +49,6 @@ RUN yum install -y \
     make \
     bc \
     file \
-    bison \
-    flex \
     patch \
     ca-certificates \
     autoconf-2.69 \
diff --git a/docker/TotalEnergies/Dockerfile b/docker/TotalEnergies/Dockerfile
@@ -38,8 +38,6 @@ RUN yum install --disablerepo=intel-mkl-repo -y \
     make \
     bc \
     file \
-    bison \
-    flex \
     patch \
     ca-certificates \
     autoconf \
diff --git a/docker/TotalEnergies/Pangea3-base.Dockerfile b/docker/TotalEnergies/Pangea3-base.Dockerfile
@@ -16,9 +16,6 @@ RUN dnf install -y \
     make \
     bc \
     file \
-    # Scotch deps \
-    bison \
-    flex \
     # vtk deps \
     patch && \
     git-lfs install #&& alternatives --set python /usr/bin/python3
diff --git a/docker/TotalEnergies/Pangea3.Dockerfile b/docker/TotalEnergies/Pangea3.Dockerfile
@@ -16,6 +16,7 @@ RUN dnf clean all && \
     dnf -y install \
         autoconf \
         automake \
+        gettext-devel \
         libtool \
         bzip2 \
         unzip
diff --git a/docker/pangea-spack.yaml b/docker/pangea-spack.yaml
@@ -25,9 +25,6 @@ spack:
       target: ppc64le
       modules: []
       environment:
-        set: # Needed for scotch
-          BISON: bison
-          FLEX: flex
         prepend_path:
           LD_LIBRARY_PATH: /data_local/sw/lsf/10.1/linux3.10-glibc2.17-ppc64le/lib
       extra_rpaths: []
@@ -89,11 +86,6 @@ spack:
       - spec: automake@1.16.1
         prefix: /usr
       buildable: false
-    bison:
-      externals:
-      - spec: bison@3.0.4
-        prefix: /usr
-      buildable: false
     bzip2:
       externals:
       - spec: bzip2@1.0.6
@@ -109,11 +101,6 @@ spack:
       - spec: cuda@11.5.0 +allow-unsupported-compilers
         prefix: /data_local/sw/cuda/11.5.0
       buildable: false
-    flex:
-      externals:
-      - spec: flex@2.6.1+lex
-        prefix: /usr
-      buildable: false
     gettext:
       externals:
       - spec: gettext@0.19.8.1
diff --git a/docker/pecan-spack.yaml b/docker/pecan-spack.yaml
@@ -15,10 +15,6 @@ spack:
   compilers::
   # Pecan CPU/GPU compiler
   - compiler:
-      environment:
-        set: # Needed for scotch
-          BISON: bison
-          FLEX: flex
       extra_rpaths: []
       flags:
         cflags: -pthread
@@ -92,12 +88,6 @@ spack:
       externals:
       - spec: automake@1.16.5
         prefix: /usr
-    bison:
-      version: [3.8.2]
-      buildable: false
-      externals:
-      - spec: bison@3.8.2
-        prefix: /usr
     cmake:
       version: [3.28.3]
       buildable: false
@@ -109,12 +99,6 @@ spack:
       externals:
       - spec: cuda@11.5.1 +allow-unsupported-compilers
         prefix: /hrtc/apps/cuda/11.5.119/x86_64/centos7
-    flex:
-      version: [2.6.4]
-      buildable: false
-      externals:
-      - spec: flex@2.6.4
-        prefix: /usr
 
     # Lock down blas, lapack implementation
     intel-mkl:
diff --git a/docker/rocky-spack.yaml b/docker/rocky-spack.yaml
@@ -14,10 +14,6 @@ spack:
 
   compilers::
   - compiler:
-      environment:
-        set: # Needed for scotch
-          BISON: bison
-          FLEX: flex
       extra_rpaths: []
       flags:
         cflags: -pthread
@@ -32,10 +28,6 @@ spack:
       spec: clang@17.0.6
       target: x86_64
   - compiler:
-      environment:
-        set: # Needed for scotch
-          BISON: bison
-          FLEX: flex
       extra_rpaths: []
       flags:
         cflags: -pthread
@@ -109,12 +101,6 @@ spack:
       externals:
       - spec: automake@1.16.5
         prefix: /usr
-    bison:
-      version: [3.8.2]
-      buildable: false
-      externals:
-      - spec: bison@3.8.2
-        prefix: /usr
     cmake:
       version: [3.28.6]
       buildable: false
@@ -128,12 +114,6 @@ spack:
         prefix: /usr/local/cuda
       - spec: cuda@12.6.3%clang@17.0.6 +allow-unsupported-compilers
         prefix: /usr/local/cuda
-    flex:
-      version: [2.6.4]
-      buildable: false
-      externals:
-      - spec: flex@2.6.4
-        prefix: /usr
     m4:
       buildable: false
       externals:
diff --git a/docker/spack.yaml b/docker/spack.yaml
@@ -14,10 +14,6 @@ spack:
 
   compilers::
   - compiler:
-      environment:
-        set: # Needed for scotch
-          BISON: bison
-          FLEX: flex
       extra_rpaths: []
       flags: {}
       modules: []
@@ -30,10 +26,6 @@ spack:
       spec: clang@15
       target: x86_64
   - compiler:
-      environment:
-        set: # Needed for scotch
-          BISON: bison
-          FLEX: flex
       extra_rpaths: []
       flags: {}
       modules: []
@@ -46,10 +38,6 @@ spack:
       spec: clang@10
       target: x86_64
   - compiler:
-      environment:
-        set: # Needed for scotch
-          BISON: bison
-          FLEX: flex
       extra_rpaths: []
       flags:
         cflags: -pthread
@@ -64,10 +52,6 @@ spack:
       spec: gcc@12
       target: x86_64
   - compiler:
-      environment:
-        set: # Needed for scotch
-          BISON: bison
-          FLEX: flex
       extra_rpaths: []
       flags:
         cflags: -pthread
@@ -82,10 +66,6 @@ spack:
       spec: gcc@11
       target: x86_64
   - compiler:
-      environment:
-        set: # Needed for scotch
-          BISON: bison
-          FLEX: flex
       extra_rpaths: []
       flags:
         cflags: -pthread
@@ -100,10 +80,6 @@ spack:
       spec: gcc@10
       target: x86_64
   - compiler:
-      environment:
-        set: # Needed for scotch
-          BISON: bison
-          FLEX: flex
       extra_rpaths: []
       flags:
         cflags: -pthread
@@ -118,10 +94,6 @@ spack:
       spec: gcc@9
       target: x86_64
   - compiler:
-      environment:
-        set: # Needed for scotch
-          BISON: bison
-          FLEX: flex
       extra_rpaths: []
       flags:
         cflags: -pthread
@@ -195,12 +167,6 @@ spack:
       externals:
       - spec: automake@1.16.5
         prefix: /usr
-    bison:
-      version: [3.8.2]
-      buildable: false
-      externals:
-      - spec: bison@3.8.2
-        prefix: /usr
     cmake:
       version: [3.28.3]
       buildable: false
@@ -212,12 +178,6 @@ spack:
       externals:
       - spec: cuda@11.8.0 +allow-unsupported-compilers
         prefix: /usr/local/cuda
-    flex:
-      version: [2.6.4]
-      buildable: false
-      externals:
-      - spec: flex@2.6.4
-        prefix: /usr
     findutils:
       version: [4.7.0]
       buildable: false
diff --git a/docker/stanford-spack.yaml b/docker/stanford-spack.yaml
@@ -28,10 +28,6 @@ spack:
         cflags: -pthread
         cxxflags: -pthread
       modules: []
-      environment:
-        set: # Needed for scotch
-          BISON: bison
-          FLEX: flex
       extra_rpaths: []
 
   packages:
@@ -92,13 +88,6 @@ spack:
       - spec: automake@1.13.4
         prefix: /usr
 
-    bison:
-      version: [3.0.4]
-      buildable: false
-      externals:
-      - spec: bison@3.0.4
-        prefix: /usr
-
     cmake:
       buildable: false
       externals:
@@ -117,12 +106,6 @@ spack:
     #  - spec: diffutils@3.3
     #    prefix: /usr
 
-    flex:
-      buildable: false
-      externals:
-      - spec: flex@2.5.37
-        prefix: /usr
-
     #gettext:
     #  buildable: false
     #  externals:
diff --git a/docker/tpl-centos-gcc-cuda.Dockerfile b/docker/tpl-centos-gcc-cuda.Dockerfile
@@ -66,8 +66,6 @@ RUN yum install -y \
     make \
     bc \
     file \
-    bison \
-    flex \
     patch \
     ca-certificates \
     autoconf \
diff --git a/docker/tpl-rockylinux-clang-cuda-12.Dockerfile b/docker/tpl-rockylinux-clang-cuda-12.Dockerfile
@@ -51,8 +51,6 @@ RUN dnf clean all && \
         tbb-devel \
         bc \
         file \
-        bison \
-        flex \
         patch \
         ca-certificates \
         autoconf \
diff --git a/docker/tpl-rockylinux-gcc-cuda-12.Dockerfile b/docker/tpl-rockylinux-gcc-cuda-12.Dockerfile
@@ -49,8 +49,6 @@ RUN dnf clean all && \
         tbb-devel \
         bc \
         file \
-        bison \
-        flex \
         patch \
         ca-certificates \
         autoconf \
diff --git a/docker/tpl-ubuntu-clang-cuda.Dockerfile b/docker/tpl-ubuntu-clang-cuda.Dockerfile
@@ -50,8 +50,6 @@ RUN apt-get install -y --no-install-recommends \
     libtbb-dev \
     bc \
     file \
-    bison \
-    flex \
     patch \
     ca-certificates \
     git
diff --git a/docker/tpl-ubuntu-clang.Dockerfile b/docker/tpl-ubuntu-clang.Dockerfile
@@ -60,8 +60,6 @@ RUN apt-get install -y --no-install-recommends \
     make \
     bc \
     file \
-    bison \
-    flex \
 # GEOS patches some tpl. Remove when it's not the case anymore.
     patch \
 # `ca-certificates`  needed by `git` to download spack repo.
diff --git a/docker/tpl-ubuntu-gcc.Dockerfile b/docker/tpl-ubuntu-gcc.Dockerfile
@@ -96,8 +96,6 @@ RUN apt-get install -y --no-install-recommends \
     make \
     bc \
     file \
-    bison \
-    flex \
 # GEOS patches some tpl. Remove when it's not the case anymore.
     patch \
 # `ca-certificates`  needed by `git` to download spack repo.
diff --git a/scripts/pygeosx_configs/blueos_3_ppc64le_ib_p9/spack.yaml b/scripts/pygeosx_configs/blueos_3_ppc64le_ib_p9/spack.yaml
@@ -115,16 +115,6 @@ spack:
       externals:
         - spec: libtool@2.4.2
           prefix: /usr
-    bison:
-      buildable: False
-      externals:
-        - spec: bison@3.0.4
-          prefix: /usr
-    flex:
-      buildable: False
-      externals:
-        - spec: flex@2.5.37
-          prefix: /usr
     tk:
       buildable: False
       externals:
diff --git a/scripts/pygeosx_configs/toss_4_x86_64_ib/spack.yaml b/scripts/pygeosx_configs/toss_4_x86_64_ib/spack.yaml
@@ -120,16 +120,6 @@ spack:
       externals:
         - spec: libtool@2.4.6
           prefix: /usr
-    bison:
-      buildable: False
-      externals:
-        - spec: bison@3.0.4
-          prefix: /usr
-    flex:
-      buildable: False
-      externals:
-        - spec: flex@2.6.1
-          prefix: /usr
     tk:
       buildable: False
       externals:
diff --git a/scripts/spack_configs/blueos_3_ppc64le_ib_p9/spack.yaml b/scripts/spack_configs/blueos_3_ppc64le_ib_p9/spack.yaml
diff --git a/scripts/spack_configs/darwin/packages.yaml b/scripts/spack_configs/darwin/packages.yaml
diff --git a/scripts/spack_configs/macOS/spack.yaml b/scripts/spack_configs/macOS/spack.yaml
diff --git a/scripts/spack_configs/pangea-3/spack.yaml b/scripts/spack_configs/pangea-3/spack.yaml
diff --git a/scripts/spack_configs/pangea-4/spack.yaml b/scripts/spack_configs/pangea-4/spack.yaml
diff --git a/scripts/spack_configs/pine/spack.yaml b/scripts/spack_configs/pine/spack.yaml
diff --git a/scripts/spack_configs/toss_4_x86_64_ib/spack.yaml b/scripts/spack_configs/toss_4_x86_64_ib/spack.yaml
