Update python3 to 3.7.6 #108
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,14 +1,14 @@ | ||
| #! /bin/bash | ||
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| #COOKIE=$(mcookie); grep -v V_GREP_ME $0 > /dev/shm/runme-$COOKIE.sh ; sleep 1; exec bash /dev/shm/runme-$COOKIE.sh $1 | ||
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| PKG=python | ||
| VERSION=3.7.6 | ||
| BUILD=0 | ||
| PYTHONVER=${VERSION%.*} | ||
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| CUDADIR=/pkg/cuda-10.2.89-1 | ||
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| PREFIX=/pkg/$PKG-$VERSION-$BUILD | ||
| if [ -n "$TESTING" ]; then PREFIX=/dev/shm/$PKG-$VERSION-$BUILD ; fi | ||
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@@ -18,7 +18,7 @@ PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin | |
| set -xe | ||
| umask 022 | ||
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| BUILD_TMPDIR=/scratch/local2/$PKG-$VERSION-$BUILD.build.tmp | ||
| test -d $BUILD_TMPDIR && ( chmod -R u+rwx $BUILD_TMPDIR || true ; rm -rf $BUILD_TMPDIR ) | ||
| mkdir -p $BUILD_TMPDIR/home | ||
| export TMPDIR=$BUILD_TMPDIR | ||
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@@ -175,7 +175,7 @@ make install | |
| python3 -m ensurepip | ||
| pip3 install --prefix=$PREFIX -I pip | ||
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| pip3 install --upgrade --prefix=$PREFIX ipython[all] | ||
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There was a problem hiding this comment. Oh, I have add this for rebuilding to find the downgrader |
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| pip3 install --prefix=$PREFIX SciPy NumPy Matplotlib pandas SymPy nose statsmodels | ||
| # clean up some dirt that statsmodels placed also into $PREFIX | ||
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@@ -217,7 +217,6 @@ pip3 install --prefix=$PREFIX louvain # monocle3 prep for Helene | |
| pip3 install --prefix=$PREFIX selenium # 19.7.19 Kreitler -> https://webxray.org/ | ||
| pip3 install --prefix=$PREFIX cooltools # Maria Valieva 17.7.2019 | ||
| pip3 install --prefix=$PREFIX gmpy # From viper context (Helpdesk Laura Glaser 9.8.2019) | ||
| pip3 install --prefix=$PREFIX torch | ||
| pip3 install --prefix=$PREFIX torchvision | ||
| pip3 install --prefix=$PREFIX plotly | ||
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@@ -231,18 +230,19 @@ pip3 install --prefix=$PREFIX threadpoolctl | |
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| pip3 install --prefix=$PREFIX pyopengl | ||
| rm -rf ${PREFIX}/lib/python$PYTHONVER/site-packages/OpenGL/Tk | ||
| # creates error, so remove it | ||
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| # pip3 install --prefix=$PREFIX HiCExplorer # Would be a nice to have, but it likes to downgrade too much, pick some cherries | ||
| pip3 install --prefix=$PREFIX HiCMatrix | ||
| pip3 install --prefix=$PREFIX pyGenomeTracks #downgrader cooler 0.8.7-> 0.8.5 | ||
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There was a problem hiding this comment. Isn’t that also the version pinned in the hic2cooler requirements? There was a problem hiding this comment. by hic2cool is the problem numpy and scipy and not cooler |
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| pip3 install --prefix=$PREFIX python-bioformats #downgrader matplotlib 3.2.0->3.1.1 docutils 0.16 -> 0.15.2 | ||
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| pip3 install --prefix=$PREFIX jupyterlab # request Peter Arndt | ||
| pip3 install --prefix=$PREFIX jupyterlab-git | ||
| pip3 install --prefix=$PREFIX libxml2-python3 # required by several bee packages after swich to python3 | ||
| pip3 install --prefix=$PREFIX scour # https://github.molgen.mpg.de/mariux64/pkg-scripts/issues/98 | ||
| pip3 install --prefix=$PREFIX multiqc | ||
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| #boost for pycuda | ||
| ( | ||
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@@ -265,24 +265,6 @@ pip3 install --prefix=$PREFIX scour # https://github.molgen.mpg.de/mar | |
| --with-python=$PREFIX/bin/python3 \ | ||
| --with-libraries=python,thread || exit 1 | ||
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| ./b2 \ | ||
| $NUMJOBS \ | ||
| --layout=system \ | ||
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@@ -304,25 +286,135 @@ pip3 install --prefix=$PREFIX scour # https://github.molgen.mpg.de/mar | |
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| #pycuda git version to get GL support | ||
| ( | ||
| PYCUDAVERS=2019.1.2 | ||
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| . ${PREFIX}/profile | ||
| cd $BUILDDIR | ||
| test -e pycuda-${PYCUDAVERS}.tar.gz || wget https://github.com/inducer/pycuda/archive/v${PYCUDAVERS}/pycuda-${PYCUDAVERS}.tar.gz | ||
| test -d pycuda-${PYCUDAVERS} || tar -xf pycuda-${PYCUDAVERS}.tar.gz | ||
| #test -d pycuda || git clone --recursive http://git.tiker.net/trees/pycuda.git | ||
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| cd pycuda-${PYCUDAVERS} | ||
| test -e siteconf.py && rm siteconf.py | ||
| python3 configure.py \ | ||
| --cuda-enable-gl \ | ||
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There was a problem hiding this comment. Please use tabs to indent this. There was a problem hiding this comment. next time I promise :-) |
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| --cuda-root=$CUDADIR \ | ||
| --no-use-shipped-boost \ | ||
| --boost-python-libname=boost_python37 \ | ||
| --boost-inc-dir=$PREFIX/include \ | ||
| --boost-lib-dir=$PREFIX/lib \ | ||
| --cudadrv-lib-dir='${CUDA_ROOT}/lib,${CUDA_ROOT}/lib/stubs' \ | ||
| --cudart-lib-dir='${CUDA_ROOT}/lib,${CUDA_ROOT}/lib/stubs' \ | ||
| --curand-lib-dir='${CUDA_ROOT}/lib,${CUDA_ROOT}/lib/stubs'\ | ||
| --ldflags=-L$PREFIX/lib | ||
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| python3 setup.py install --prefix $PREFIX | ||
| ) | ||
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| # hic2cool from source to stop downgrading python packages | ||
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There was a problem hiding this comment. Which requirements are a problem? |
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| ( | ||
| HICVERS=0.8.0 | ||
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| . ${PREFIX}/profile | ||
| cd $BUILDDIR | ||
| test -e hic2cool-${HICVERS}.tar.gz || wget https://github.com/4dn-dcic/hic2cool/archive/${HICVERS}/hic2cool-${HICVERS}.tar.gz | ||
| test -d hic2cool-${HICVERS} || tar -xf hic2cool-${HICVERS}.tar.gz | ||
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| cd hic2cool-${HICVERS} | ||
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| if $( grep '==' requirements.txt >/dev/null ); then | ||
| patch -p1 <<'EOFHIC' | ||
| diff --git a/requirements.txt b/requirements.txt | ||
| index d7e701b..9d3a01c 100644 | ||
| --- a/requirements.txt | ||
| +++ b/requirements.txt | ||
| @@ -1,5 +1,5 @@ | ||
| -h5py==2.8.0 | ||
| -pandas==0.24.2 | ||
| -numpy==1.16.3 | ||
| -scipy==1.2.1 | ||
| -cooler==0.8.5 | ||
| +h5py | ||
| +pandas | ||
| +numpy | ||
| +scipy | ||
| +cooler | ||
| EOFHIC | ||
| fi | ||
| pip3 install -r requirements.txt --prefix ${PREFIX} | ||
| python3 setup.py install --prefix ${PREFIX} | ||
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There was a problem hiding this comment. https://github.com/4dn-dcic/hic2cool/pull/44#issuecomment-605348278 claims, |
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| ) | ||
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| #tensorflow | ||
| ( | ||
| TFVERSION=2.1.0 | ||
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There was a problem hiding this comment. Why do we need to install Tensorflow from source? Why is the package not good enough? There was a problem hiding this comment. f.e. the half of the cluster dont work with the pip package |
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| TFSRC=https://github.com/tensorflow/tensorflow/archive/v${TFVERSION}/tensorflow-${TFVERSION}.tar.gz | ||
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| . ${PREFIX}/profile | ||
| . /pkg/bazel-0.28.1-0/profile | ||
| cd $BUILDDIR | ||
| test -e tensorflow-${TFVERSION}.tar.gz || wget $TFSRC | ||
| test -d tensorflow-${TFVERSION} || tar -xf tensorflow-${TFVERSION}.tar.gz | ||
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| cd tensorflow-${TFVERSION} | ||
| #vars for config | ||
| export PYTHON_BIN_PATH=${PREFIX}/bin/python3 | ||
| export USE_DEFAULT_PYTHON_LIB_PATH=1 | ||
| export TF_NEED_JEMALLOC=1 | ||
| export TF_NEED_KAFKA=0 | ||
| export TF_NEED_OPENCL_SYCL=0 | ||
| export TF_NEED_AWS=0 | ||
| export TF_NEED_GCP=0 | ||
| export TF_NEED_HDFS=0 | ||
| export TF_NEED_S3=0 | ||
| export TF_ENABLE_XLA=1 | ||
| export TF_NEED_GDR=0 | ||
| export TF_NEED_VERBS=0 | ||
| export TF_NEED_OPENCL=0 | ||
| export TF_NEED_MPI=0 | ||
| export TF_NEED_TENSORRT=1 | ||
| export TF_NEED_NGRAPH=0 | ||
| export TF_NEED_IGNITE=0 | ||
| export TF_NEED_ROCM=0 | ||
| export TF_SET_ANDROID_WORKSPACE=0 | ||
| export TF_DOWNLOAD_CLANG=0 | ||
| export TF_NCCL_VERSION=2.5 | ||
| export TF_IGNORE_MAX_BAZEL_VERSION=1 | ||
| export NCCL_INSTALL_PATH=${CUDADIR} | ||
| export GCC_HOST_COMPILER_PATH=/usr/bin/gcc | ||
| export TF_CUDA_CLANG=0 | ||
| export CLANG_CUDA_COMPILER_PATH=/usr/bin/clang | ||
| export TF_CUDA_PATHS=${CUDADIR},${CUDADIR}/extras/CUPTI,${CUDADIR}/nvvm | ||
| export TF_CUDA_VERSION=$(${CUDADIR}/bin/nvcc --version | sed -n 's/^.*release \(.*\),.*/\1/p') | ||
| export TF_CUDNN_VERSION=$(sed -n 's/^#define CUDNN_MAJOR\s*\(.*\).*/\1/p' ${CUDADIR}/include/cudnn.h) | ||
| export TF_CUDA_COMPUTE_CAPABILITIES=3.5,3.7,5.0,5.2,5.3,6.0,6.1,6.2,7.0,7.2,7.5 | ||
| export CC_OPT_FLAGS="-march=nehalem" | ||
| export TF_NEED_CUDA=1 | ||
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| ./configure | ||
| bazel build \ | ||
| --cxxopt="-march=nehalem" \ | ||
| --copt="-march=nehalem" \ | ||
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There was a problem hiding this comment. Do all our servers support this? There was a problem hiding this comment. No, but the important do it. This activate SSE4.1 There was a problem hiding this comment. if you want I can send you the full list |
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| //tensorflow:libtensorflow.so \ | ||
| //tensorflow:libtensorflow_cc.so \ | ||
| //tensorflow:install_headers \ | ||
| //tensorflow/tools/pip_package:build_pip_package | ||
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| test -d tensorflow-pip && rm -r tensorflow-pip | ||
| mkdir tensorflow-pip | ||
| ./bazel-bin/tensorflow/tools/pip_package/build_pip_package --src ${BUILDDIR}/tensorflow-pip | ||
| cd ${BUILDDIR} | ||
| #remove symlinks into TMPDIR | ||
| test -e tensorflow-pip.tar && rm tensorflow-pip.tar | ||
| tar -chf tensorflow-pip.tar tensorflow-pip | ||
| test -d tensorflow-pip && rm -r tensorflow-pip | ||
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| tar -xf tensorflow-pip.tar | ||
| cd ${BUILDDIR}/tensorflow-pip | ||
| python3 setup.py build | ||
| python3 setup.py install --prefix $PREFIX | ||
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| ) | ||
| # try to load all packages, maybe we can see installation errors | ||
| python3 -c 'help("modules")' > /dev/null | ||
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Why is that not needed anymore? It’d be great if you mentioned that in the commit message (and also prefix it with
python-3.7.6:). Maybe even delete that line.There was a problem hiding this comment.
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is a dev line
copy the script to /dev/shm and run there
so you can edit while building