Fix some build issues - supporess MPI (#24)

README.md

@@ -183,6 +183,9 @@ There is an install run target built into the BUILD files, and you must
 decide upon the directory to which that target should copy executables.
 See previous section.
 
+While there is a script that should do the build for you, underneath these
+are the commands being issued. Skip to the next section unless interested.
+
 A typical build command might be (change the path for test_env)
 
 ```
@@ -212,6 +215,8 @@ version will be allowed to float via bazelisk.
 
 ## Targets to Test and Build
 
+First run `build_third_party.sh` to ensure dependencies are built.
+
 Actual tests, builds and installs can be handled by the `build_from_src.sh` script.
 
 The script `build_from_src.sh` will
@@ -221,9 +226,9 @@ The script `build_from_src.sh` will
 3. install executables into the `bin/Linux` directory (build_deps/install.bzl)
 
 ## cmake
-There is `cmake` infrasture
+There is `cmake` infrastructure
 included, but that may, or may not, work - within Lilly we have not
-been able to make that work, usually as a result of conflicting protcol buffer
+been able to make it work, usually as a result of conflicting protcol buffer
 versions on the system, but externally it often works, although it has not
 been tested recently.
 
@@ -240,7 +245,11 @@ cd ./src
 # cp /tmp/WORKSPACE WORKSPACE
 # Examine /tmp/install.bzl
 # cp /tmp/install.bzl build_deps
+./build_from_src.sh
 
 # Rebuild Molecule_Tools any time
 bazelisk --output_user_root=/node/scratch/$USER build --jobs=8 --enable_bzlmod --experimental_cc_shared_library -c opt --cxxopt=-DGIT_HASH=\"$(git rev-parse --short --verify HEAD)\" --cxxopt=-DTODAY=\"$(date +%Y-%b-%d)\" //Molecule_Tools:all --test_env=C3TK_DATA_PERSISTENT=/full/path/to/LillyMol/queries
-```
+```
+Note that because the date is included with cxxopt, this _will_ cause a daily
+recompile. While this is hardly desirable, knowing when an executable was compiled
+can be useful.

docs/python/LillyMolPython.md

@@ -54,7 +54,7 @@ This works because the LillyMol Molecule is a very lazy object. It never compute
 things like fragment membership, ring membership, aromaticity or canononical
 ordering unless requested. So if you remove an atom, or bond, it will destroy any
 information it has about those derived quantities. Only if requested will any
-be computed.
+be recomputed.
 
 This has many advantages. For example if a molecle is built from a smiles
 and then the only thing ever requested is the number of atoms, that will be
@@ -593,13 +593,13 @@ m = MolFromSmiles('C(=N)(C1=C(O)C(=C(O)C=C1O)OC)CC1=CC=C(O)C=C1 CHEMBL503634')
 query.substructure_search(m)
 ```
 The number of matches will be returned. In this case it will frequently be 2 since
-the query will mactch two times in a benzene like ring.
+the query will match two times in a benzene like ring.
 
 To get the matched atoms, as a List of List's,
 ```
 matches = q.substructure_search_matches(m)
 ```
-and then the matches can be iterated.
+and then the matches object (type SubstructureResults) can be iterated.
 
 For example if you wanted to place an isotope on each set of matched atoms that might look like
 ```
@@ -608,7 +608,7 @@ for match in query.substructure_search_matches(m):
   m.set_isotopes(match, 1)
   print(m)
 ```
-Omit the `remove_isotopes` call to accumulate the results.
+Omit the `remove_isotopes` call to add the new isotopes to whatever might have already been there.
 
 On the other hand if you need to know which matched atom is which, that might look like
 ```
@@ -660,7 +660,7 @@ or
 ```
 If the reaction is a simple form that has either no sidechains,
 or all sidechains have a single, already specified, reagent, then
-the `in_place_transformations1 method can be used.
+the `in_place_transformations` method can be used.
 ```
   rxn.in_place_transformations(m)
 ```

src/Molecule_Tools/BUILD

@@ -353,23 +353,6 @@ cc_proto_library(
     ],
 )
 
-proto_library(
-    name = "tsubstructure_proto",
-    srcs = [
-        "tsubstructure.proto",
-    ],
-    deps = [
-        "//Molecule_Lib:substructure_proto",
-    ],
-)
-
-cc_proto_library(
-    name = "tsubstructure_cc_proto",
-    deps = [
-        "tsubstructure_proto",
-    ],
-)
-
 proto_library(
     name = "xlogp_proto",
     srcs = [
@@ -2852,22 +2835,22 @@ cc_library(
 #    ],
 #)
 
-cc_library(
-    name = "unique_molecules_api",
-    srcs = [
-        "unique_molecules_api.cc",
-    ],
-    hdrs = [
-        "unique_molecules_api.h",
-    ],
-    deps = [
-        "//Molecule_Lib:iwmolecule",
-        "@com_google_absl//absl/container:btree",
-    ],
-    visibility = [
-        "//visibility:public",
-    ],
-)
+# cc_library(
+#     name = "unique_molecules_api",
+#     srcs = [
+#         "unique_molecules_api.cc",
+#     ],
+#     hdrs = [
+#         "unique_molecules_api.h",
+#     ],
+#     deps = [
+#         "//Molecule_Lib:iwmolecule",
+#         "@com_google_absl//absl/container:btree",
+#     ],
+#     visibility = [
+#         "//visibility:public",
+#     ],
+# )
 
 cc_library(
     name = "xlogp_lib",

src/Utilities/GFP_Tools/BUILD

@@ -315,23 +315,24 @@ cc_binary(
     ],
 )
 
-cc_binary(
-    name = "gfp_leader_threaded_mpi",
-    srcs = [
-        "gfp_leader_threaded_mpi.cc",
-    ],
-    tags = [
-        "mpi",
-    ],
-    deps = [
-        "//Foundational/accumulator",
-        "//Foundational/cmdline:iwcmdline",
-        "//Foundational/data_source:iwstring_data_source",
-        "//Foundational/iwmisc",
-        "//Utilities/GFP_Tools:gfp",
-        "@mpich",
-    ],
-)
+# Enable if MPI is enabled in the current environment.
+# cc_binary(
+#     name = "gfp_leader_threaded_mpi",
+#     srcs = [
+#         "gfp_leader_threaded_mpi.cc",
+#     ],
+#     tags = [
+#         "mpi",
+#     ],
+#     deps = [
+#         "//Foundational/accumulator",
+#         "//Foundational/cmdline:iwcmdline",
+#         "//Foundational/data_source:iwstring_data_source",
+#         "//Foundational/iwmisc",
+#         "//Utilities/GFP_Tools:gfp",
+#         "@mpich",
+#     ],
+# )
 
 cc_binary(
     name = "gfp_mcs",

src/build_from_src.sh

@@ -17,7 +17,11 @@ jobs='8'
 # bazel will not work on an NFS mounted file system. So if you are on an NFS
 # file system, you must specify a value for --output_user_root that is
 # locally mounted.
-bazel_options="--output_user_root=/node/scratch/ian"
+# If your local file system is suitable for the bazel cache.
+bazel_options=""
+# If inside Lilly, some local scratch storage
+# bazel_options="--output_user_root=/node/scratch/ian"
+
 build_options="--cxxopt=-DGIT_HASH=\"$(git rev-parse --short --verify HEAD)\" --cxxopt=-DTODAY=\"$(date +%Y-%b-%d)\" --jobs=${jobs} -c opt --enable_bzlmod --experimental_cc_shared_library"
 
 echo ${common_options}