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Compile rdkit (#4442)

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`rdkit` extension

```
postgres=# create extension rdkit;
CREATE EXTENSION
postgres=# select 'c1[o,s]ncn1'::qmol;
    qmol
-------------
 c1[o,s]ncn1
(1 row)
```
This commit is contained in:
Vadim Kharitonov
2023-06-12 11:13:33 +02:00
committed by GitHub
parent 7e17979d7a
commit e9072ee178
1 changed files with 62 additions and 6 deletions
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68
Dockerfile.compute-node
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@@ -67,7 +67,7 @@ RUN apt update && \
RUN wget https://gitlab.com/Oslandia/SFCGAL/-/archive/v1.3.10/SFCGAL-v1.3.10.tar.gz -O SFCGAL.tar.gz && \
echo "4e39b3b2adada6254a7bdba6d297bb28e1a9835a9f879b74f37e2dab70203232 SFCGAL.tar.gz" | sha256sum --check && \
mkdir sfcgal-src && cd sfcgal-src && tar xvzf ../SFCGAL.tar.gz --strip-components=1 -C . && \
cmake . && make -j $(getconf _NPROCESSORS_ONLN) && \
cmake -DCMAKE_BUILD_TYPE=Release . && make -j $(getconf _NPROCESSORS_ONLN) && \
DESTDIR=/sfcgal make install -j $(getconf _NPROCESSORS_ONLN) && \
make clean && cp -R /sfcgal/* /
@@ -95,7 +95,7 @@ RUN wget https://github.com/pgRouting/pgrouting/archive/v3.4.2.tar.gz -O pgrouti
mkdir pgrouting-src && cd pgrouting-src && tar xvzf ../pgrouting.tar.gz --strip-components=1 -C . && \
mkdir build && \
cd build && \
cmake .. && \
cmake -DCMAKE_BUILD_TYPE=Release .. && \
make -j $(getconf _NPROCESSORS_ONLN) && \
make -j $(getconf _NPROCESSORS_ONLN) install && \
echo 'trusted = true' >> /usr/local/pgsql/share/extension/pgrouting.control
@@ -355,7 +355,7 @@ RUN apt-get update && \
wget https://github.com/timescale/timescaledb/archive/refs/tags/2.10.1.tar.gz -O timescaledb.tar.gz && \
echo "6fca72a6ed0f6d32d2b3523951ede73dc5f9b0077b38450a029a5f411fdb8c73 timescaledb.tar.gz" | sha256sum --check && \
mkdir timescaledb-src && cd timescaledb-src && tar xvzf ../timescaledb.tar.gz --strip-components=1 -C . && \
./bootstrap -DSEND_TELEMETRY_DEFAULT:BOOL=OFF -DUSE_TELEMETRY:BOOL=OFF -DAPACHE_ONLY:BOOL=ON && \
./bootstrap -DSEND_TELEMETRY_DEFAULT:BOOL=OFF -DUSE_TELEMETRY:BOOL=OFF -DAPACHE_ONLY:BOOL=ON -DCMAKE_BUILD_TYPE=Release && \
cd build && \
make -j $(getconf _NPROCESSORS_ONLN) && \
make install -j $(getconf _NPROCESSORS_ONLN) && \
@@ -410,7 +410,7 @@ RUN apt-get update && \
mkdir kq_imcx-src && cd kq_imcx-src && tar xvzf ../kq_imcx.tar.gz --strip-components=1 -C . && \
mkdir build && \
cd build && \
cmake .. && \
cmake -DCMAKE_BUILD_TYPE=Release .. && \
make -j $(getconf _NPROCESSORS_ONLN) && \
make -j $(getconf _NPROCESSORS_ONLN) install && \
echo 'trusted = true' >> /usr/local/pgsql/share/extension/kq_imcx.control
@@ -432,6 +432,54 @@ RUN wget https://github.com/citusdata/pg_cron/archive/refs/tags/v1.5.2.tar.gz -O
make -j $(getconf _NPROCESSORS_ONLN) install && \
echo 'trusted = true' >> /usr/local/pgsql/share/extension/pg_cron.control
#########################################################################################
#
# Layer "rdkit-pg-build"
# compile rdkit extension
#
#########################################################################################
FROM build-deps AS rdkit-pg-build
COPY --from=pg-build /usr/local/pgsql/ /usr/local/pgsql/
RUN apt-get update && \
apt-get install -y \
cmake \
libboost-iostreams1.74-dev \
libboost-regex1.74-dev \
libboost-serialization1.74-dev \
libboost-system1.74-dev \
libeigen3-dev \
libfreetype6-dev
ENV PATH "/usr/local/pgsql/bin/:/usr/local/pgsql/:$PATH"
RUN wget https://github.com/rdkit/rdkit/archive/refs/tags/Release_2023_03_1.tar.gz -O rdkit.tar.gz && \
echo "db346afbd0ba52c843926a2a62f8a38c7b774ffab37eaf382d789a824f21996c rdkit.tar.gz" | sha256sum --check && \
mkdir rdkit-src && cd rdkit-src && tar xvzf ../rdkit.tar.gz --strip-components=1 -C . && \
cmake \
-D RDK_BUILD_CAIRO_SUPPORT=OFF \
-D RDK_BUILD_INCHI_SUPPORT=ON \
-D RDK_BUILD_AVALON_SUPPORT=ON \
-D RDK_BUILD_PYTHON_WRAPPERS=OFF \
-D RDK_BUILD_DESCRIPTORS3D=OFF \
-D RDK_BUILD_FREESASA_SUPPORT=OFF \
-D RDK_BUILD_COORDGEN_SUPPORT=ON \
-D RDK_BUILD_MOLINTERCHANGE_SUPPORT=OFF \
-D RDK_BUILD_YAEHMOP_SUPPORT=OFF \
-D RDK_BUILD_STRUCTCHECKER_SUPPORT=OFF \
-D RDK_USE_URF=OFF \
-D RDK_BUILD_PGSQL=ON \
-D RDK_PGSQL_STATIC=ON \
-D PostgreSQL_CONFIG=pg_config \
-D PostgreSQL_INCLUDE_DIR=`pg_config --includedir` \
-D PostgreSQL_TYPE_INCLUDE_DIR=`pg_config --includedir-server` \
-D PostgreSQL_LIBRARY_DIR=`pg_config --libdir` \
-D RDK_INSTALL_INTREE=OFF \
-D CMAKE_BUILD_TYPE=Release \
. && \
make -j $(getconf _NPROCESSORS_ONLN) && \
make -j $(getconf _NPROCESSORS_ONLN) install && \
echo 'trusted = true' >> /usr/local/pgsql/share/extension/rdkit.control
#########################################################################################
#
# Layer "rust extensions"
@@ -564,6 +612,7 @@ COPY --from=pg-hint-plan-pg-build /usr/local/pgsql/ /usr/local/pgsql/
COPY --from=kq-imcx-pg-build /usr/local/pgsql/ /usr/local/pgsql/
COPY --from=pg-cron-pg-build /usr/local/pgsql/ /usr/local/pgsql/
COPY --from=pg-pgx-ulid-build /usr/local/pgsql/ /usr/local/pgsql/
COPY --from=rdkit-pg-build /usr/local/pgsql/ /usr/local/pgsql/
COPY pgxn/ pgxn/
RUN make -j $(getconf _NPROCESSORS_ONLN) \
@@ -637,14 +686,19 @@ COPY --from=compute-tools --chown=postgres /home/nonroot/target/release-line-deb
# libgeos, libgdal, libsfcgal1, libproj and libprotobuf-c1 for PostGIS
# libxml2, libxslt1.1 for xml2
# libzstd1 for zstd
# libboost*, libfreetype6, and zlib1g for rdkit
RUN apt update && \
apt install --no-install-recommends -y \
gdb \
locales \
libicu67 \
liblz4-1 \
libreadline8 \
libboost-iostreams1.74.0 \
libboost-regex1.74.0 \
libboost-serialization1.74.0 \
libboost-system1.74.0 \
libossp-uuid16 \
libfreetype6 \
libgeos-c1v5 \
libgdal28 \
libproj19 \
@@ -654,7 +708,9 @@ RUN apt update && \
libxslt1.1 \
libzstd1 \
libcurl4-openssl-dev \
procps && \
locales \
procps \
zlib1g && \
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
localedef -i en_US -c -f UTF-8 -A /usr/share/locale/locale.alias en_US.UTF-8