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lindemann09/install_CmdStan.sh

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CmdStan installation script for Debian Linux
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install_CmdStan.sh
#!/bin/bash
#
# Linux installation script for CmdStan (http://mc-stan.org/)
# Downloads and installs CmdStan on DEBIAN/UBUNTU LINUX
# The following shell commands will be created (/usr/bin/...):
# stanc
# stan_make
# stan_print
#
# Please adapt VERSION number!
#
# (c) O. Lindemann, U Potsdam
VERSION=2.6.2
# dependencies
sudo apt-get install curl libxml2-dev
# download
cd /tmp
wget https://github.com/stan-dev/cmdstan/releases/download/v${VERSION}/cmdstan-${VERSION}.tar.gz
# extract
tar xzf cmdstan-${VERSION}.tar.gz
cd cmdstan-${VERSION}
# make
make build -j2
cd /tmp
# move to cmdStan to /opt
sudo rm -rf /opt/cmdstan-${VERSION}
sudo mv cmdstan-${VERSION} /opt/
# STANC
sudo ln -fs /opt/cmdstan-${VERSION}/bin/stanc /usr/bin
# STAN_PRINT
sudo ln -fs /opt/cmdstan-${VERSION}/bin/print /usr/bin/stan_print
# STAN_MAKE
STANMAKE=/opt/cmdstan-${VERSION}/bin/stan_make
TMP=/tmp/stan_make.tmp.sh
echo "#!/bin/bash" > ${TMP}
echo "#" >> ${TMP}
echo "# Bash script for compiling stan models" >> ${TMP}
echo "# Usage: stan_make.sh <stan model file>" >> ${TMP}
echo "#" >> ${TMP}
echo "# (c) O. Lindemann" >> ${TMP}
echo "" >> ${TMP}
echo "STAN_FOLDER=/opt/cmdstan-${VERSION}/" >> ${TMP}
echo "" >> ${TMP}
echo "FILE=\$(realpath \${1})" >> ${TMP}
echo "DIR=\${FILE%/*} " >> ${TMP}
echo "FLNAME=\${FILE##*/}" >> ${TMP}
echo "FLNAME_NO_SUFFIX=\${FLNAME%.*}" >> ${TMP}
echo "# complile from stan folder" >> ${TMP}
echo "cd \$STAN_FOLDER" >> ${TMP}
echo "make \${DIR}/\${FLNAME_NO_SUFFIX}" >> ${TMP}
chmod +x ${TMP}
sudo mv ${TMP} ${STANMAKE}
sudo ln -fs ${STANMAKE} /usr/bin
@isosphere
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isosphere commented Oct 17, 2022 •
edited
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Sadly does not seem to compile nicely on Debian bullseye:

make[1]: Entering directory '/tmp/cmdstan-2.30.1/stan/lib/stan_math/lib/tbb'
g++ -c -MMD -O2 -g -DDO_ITT_NOTIFY -DUSE_PTHREAD -pthread -m64 -mrtm   -Wno-unknown-warning-option -Wno-deprecated-copy -Wno-missing-attributes -Wno-class-memaccess -Wno-sized-deallocation   -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fno-rtti -fno-exceptions -D__TBBMALLOC_BUILD=1 -Wno-parentheses -Wno-sized-deallocation -fPIC -flifetime-dse=1 -I../tbb_2020.3/src -I../tbb_2020.3/src/rml/include -I../tbb_2020.3/include -I../tbb_2020.3/src/tbbmalloc -I../tbb_2020.3/src/tbbmalloc ../tbb_2020.3/src/tbbmalloc/backend.cpp
In file included from ../tbb_2020.3/include/tbb/tbb_config.h:36,
                 from ../tbb_2020.3/include/tbb/tbb_stddef.h:91,
                 from ../tbb_2020.3/src/tbbmalloc/Customize.h:21,
                 from ../tbb_2020.3/src/tbbmalloc/TypeDefinitions.h:54,
                 from ../tbb_2020.3/src/tbbmalloc/tbbmalloc_internal.h:21,
                 from ../tbb_2020.3/src/tbbmalloc/backend.cpp:19:
/usr/include/c++/10/cstddef:49:10: fatal error: bits/c++config.h: No such file or directory
   49 | #include <bits/c++config.h>
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
make[1]: *** [/tmp/cmdstan-2.30.1/stan/lib/stan_math/lib/tbb_2020.3/build/Makefile.tbbmalloc:65: backend.o] Error 1
make[1]: Leaving directory '/tmp/cmdstan-2.30.1/stan/lib/stan_math/lib/tbb'
make: *** [stan/lib/stan_math/make/libraries:173: stan/lib/stan_math/lib/tbb/tbbmalloc.def] Error 2
make: *** Waiting for unfinished jobs....

this search implies that libstdc++-10-dev should provide it, but this does not avail me. I'll try to remember to update this comment if I figure it out.

The cstddef file that triggers this lives in /usr/include/c++/10/, which does contain a bits folder but not with that file. The file it wants is in /usr/include/i386-linux-gnu/c++/10/bits.

this discussion looks relevant. It seems on Debian with this version of cmdstan we're using the wrong stdlib; libstdc++ has the includes I need but I am struggling to force Stan to use it, which the linked discussion suggests will work.

I have discovered I can affect this stage by editing stan/lib/stan_math/lib/tbb_2020.3/build/Makefile.tbbmalloc, but this has not helped yet. I think -stdver is the flag I want to manipulate.

I've tried to build tbb with clang instead of g++ with make compiler=clang but I get the same error, just from a different compiler. I can however change the behaviour by specifying make compiler=clang CXXFLAGS+=-stdlib=libc++ upon which now #include <cstddef> fails.

I've asked on the Stan discourse: https://discourse.mc-stan.org/t/unable-to-build-cmdstan-2-30-1-on-debian-bullseye-bits-c-config-h-tbbmalloc/29149

e: Solved, see above discourse link for solution.

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