HansBartelmess
commented
2 years ago Update when loading all the modules on the desktop there is a different error:
module load gcc/9.4.0 git/2.26.0 boost/1.69.0 htslib/1.11.0 gmp/6.1.0 cmake/3.20.5 curl/7.77.0 miniconda/4.9.2
-- Found Boost: /software/boost/1.69.0/include (found suitable version "1.69.0", minimum required is "1.65") found components: system filesystem program_options date_time log_setup log iostreams timer thread regex chrono atomic
-- Boost include dir: /software/boost/1.69.0/include
-- Boost libraries: /software/boost/1.69.0/lib/libboost_system.so/software/boost/1.69.0/lib/libboost_filesystem.so/software/boost/1.69.0/lib/libboost_program_options.so/software/boost/1.69.0/lib/libboost_date_time.so/software/boost/1.69.0/lib/libboost_log_setup.so/software/boost/1.69.0/lib/libboost_log.so/software/boost/1.69.0/lib/libboost_iostreams.so/software/boost/1.69.0/lib/libboost_timer.so/software/boost/1.69.0/lib/libboost_thread.so-pthread/software/boost/1.69.0/lib/libboost_regex.so/software/boost/1.69.0/lib/libboost_chrono.so/software/boost/1.69.0/lib/libboost_atomic.so
-- GMP_INCLUDES=GMP_INCLUDES-NOTFOUND
CMake Error at /software/cmake/3.20.5/share/cmake-3.20/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
Could NOT find GMP (missing: GMP_INCLUDES GMP_LIBRARIES GMP_VERSION_OK)
(Required is at least version "5.1.0")
Call Stack (most recent call first):
/software/cmake/3.20.5/share/cmake-3.20/Modules/FindPackageHandleStandardArgs.cmake:594 (_FPHSA_FAILURE_MESSAGE)
build/cmake/modules/FindGMP.cmake:74 (find_package_handle_standard_args)
src/CMakeLists.txt:782 (find_package)
-- Configuring incomplete, errors occurred!
See also "/data/octopus/build/CMakeFiles/CMakeOutput.log".
See also "/data/octopus/build/CMakeFiles/CMakeError.log".When we check the ENV variables they are set correctly:
-bash-4.2$ echo $GMP_INCLUDES
/software/gmp/6.1.0/include
-bash-4.2$ echo $GMP_LIBRARIES
/software/gmp/6.1.0/libso not only those 2 need to be explicitly set by the installer options:
octopus/scripts/install.py --dependencies --forests --prefix=/data/hans/oct --gmp=/software/gmp/6.1.0 --htslib=/software/htslib/1.11.0
-- GMP_INCLUDES=/software/gmp/6.1.0/include
-- Found GMP: /software/gmp/6.1.0/include (Required is at least version "5.1.0")
-- GMP include dir: /software/gmp/6.1.0/include
-- GMP libraries: /software/gmp/6.1.0/lib/libgmp.so
-- Found HTSlib
-- HTSlib include dirs: /software/htslib/1.11.0/include
-- HTSlib libraries: /software/htslib/1.11.0/lib/libhts.so
-- IPO is supported!
-- Configuring done
-- Generating done
-- Build files have been written to: /data/octopus/build
Installing Octopus 0.7.4 (master ed012a6e)He found them! but instead of 34% he fails at 35%:
[ 35%] Building CXX object src/CMakeFiles/octopus.dir/core/callers/individual_caller.cpp.o
In Datei, eingebunden von /software/boost/1.69.0/include/boost/multiprecision/traits/is_variable_precision.hpp:10,
von /software/boost/1.69.0/include/boost/multiprecision/detail/precision.hpp:9,
von /software/boost/1.69.0/include/boost/multiprecision/number.hpp:23,
von /software/boost/1.69.0/include/boost/multiprecision/cpp_dec_float.hpp:29,
von /data/octopus/src/basics/phred.hpp:16,
von /data/octopus/src/core/callers/cancer_caller.hpp:24,
von /data/octopus/src/core/callers/cancer_caller.cpp:4:
/software/boost/1.69.0/include/boost/multiprecision/detail/default_ops.hpp: In Instanziierung von »typename boost::enable_if_c<(boost::multiprecision::number_category<Num>::value == boost::multiprecision::number_kind_floating_point), boost::multiprecision::number<Backend, ExpressionTemplates> >::type boost::multiprecision::frexp(const boost::multiprecision::number<Backend, ExpressionTemplates>&, int*) [with T = boost::multiprecision::backends::gmp_float<1000>; boost::multiprecision::expression_template_option ExpressionTemplates = boost::multiprecision::et_on; typename boost::enable_if_c<(boost::multiprecision::number_category<Num>::value == boost::multiprecision::number_kind_floating_point), boost::multiprecision::number<Backend, ExpressionTemplates> >::type = boost::multiprecision::number<boost::multiprecision::backends::gmp_float<1000> >]«:
/software/boost/1.69.0/include/boost/math/special_functions/next.hpp:205:21: erfordert durch »T boost::math::detail::float_next_imp(const T&, const true_&, const Policy&) [with T = boost::multiprecision::number<boost::multiprecision::backends::gmp_float<1000> >; Policy = boost::math::policies::policy<boost::math::policies::domain_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::evaluation_error<boost::math::policies::errno_on_error>, boost::math::policies::rounding_error<boost::math::policies::errno_on_error> >; mpl_::true_ = mpl_::bool_<true>]«
/software/boost/1.69.0/include/boost/math/special_functions/next.hpp:267:33: erfordert durch »typename boost::math::tools::promote_args<T>::type boost::math::float_next(const T&, const Policy&) [with T = boost::multiprecision::number<boost::multiprecision::backends::gmp_float<1000> >; Policy = boost::math::policies::policy<boost::math::policies::domain_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::evaluation_error<boost::math::policies::errno_on_error>, boost::math::policies::rounding_error<boost::math::policies::errno_on_error> >; typename boost::math::tools::promote_args<T>::type = boost::multiprecision::number<boost::multiprecision::backends::gmp_float<1000> >]«
/software/boost/1.69.0/include/boost/math/special_functions/next.hpp:435:65: erfordert durch »typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::nextafter(const T&, const U&, const Policy&) [with T = boost::multiprecision::number<boost::multiprecision::backends::gmp_float<1000> >; U = boost::multiprecision::number<boost::multiprecision::backends::gmp_float<1000> >; Policy = boost::math::policies::policy<boost::math::policies::domain_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::evaluation_error<boost::math::policies::errno_on_error>, boost::math::policies::rounding_error<boost::math::policies::errno_on_error> >; typename boost::math::tools::promote_args<RT1, RT2>::type = boost::multiprecision::number<boost::multiprecision::backends::gmp_float<1000> >]«
/software/boost/1.69.0/include/boost/multiprecision/detail/default_ops.hpp:2374:36: erfordert durch »boost::multiprecision::number<Backend, ExpressionTemplates> boost::multiprecision::nextafter(const boost::multiprecision::number<Backend, ExpressionTemplates>&, const boost::multiprecision::number<Backend, ExpressionTemplates>&) [with Backend = boost::multiprecision::backends::gmp_float<1000>; boost::multiprecision::expression_template_option ExpressionTemplates = boost::multiprecision::et_on]«
/data/octopus/src/basics/phred.hpp:103:62: erfordert durch »octopus::Phred<Q> octopus::probability_true_to_phred(boost::multiprecision::number<From>) [with T = double; Backend = boost::multiprecision::backends::gmp_float<1000>; typename std::enable_if<std::is_arithmetic<_Tp>::value, void>::type = void]«
/data/octopus/src/core/callers/cancer_caller.cpp:932:61: von hier erfordert
/software/boost/1.69.0/include/boost/multiprecision/detail/number_base.hpp:151:39: Fehler: das Verschieben eines lokalen Objekts in einer return-Anweisung verhindert das Einsparen der Kopie [-Werror=pessimizing-move]
151 | # define BOOST_MP_MOVE(x) std::move(x)
| ^
/software/boost/1.69.0/include/boost/multiprecision/detail/default_ops.hpp:2708:11: Anmerkung: bei Substitution des Makros »BOOST_MP_MOVE«
2708 | return BOOST_MP_MOVE(result);
| ^~~~~~~~~~~~~
/software/boost/1.69.0/include/boost/multiprecision/detail/number_base.hpp:151:39: Anmerkung: entfernen Sie den Aufruf von »std::move«
151 | # define BOOST_MP_MOVE(x) std::move(x)
| ^
/software/boost/1.69.0/include/boost/multiprecision/detail/default_ops.hpp:2708:11: Anmerkung: bei Substitution des Makros »BOOST_MP_MOVE«
2708 | return BOOST_MP_MOVE(result);
| ^~~~~~~~~~~~~
[ 35%] Building CXX object src/CMakeFiles/octopus.dir/core/callers/population_caller.cpp.o
[ 35%] Building CXX object src/CMakeFiles/octopus.dir/core/callers/trio_caller.cpp.o
[ 36%] Building CXX object src/CMakeFiles/octopus.dir/core/callers/polyclone_caller.cpp.oSeems to be stuck from there running into a state where the RAM and swap are completely filled up
So far from me today.
Regards, Hans
dancooke
For all centos cluster admins go to the last entry for install instructions.
Dear Developers of octopus
We got a request from a user of our cluster system to make octopus available as a module. We are working with a module based software stack to make it easy for the user to just load and use the software. Also this gives us a solution to manage software centrally as admins and saves a lot of disc space. I am sorry for the long text after this line, but i wanted to describe and show the problems clearly.
I tried the different ways of installing octopus. And the conda way seems to be only supporting ubuntu.
1. way Our build host with cmake
All the prerequisites are satisfied it seems....
cmake -DCMAKE_INSTALL_PREFIX:PATH=/software/octopus/0.7.4 ..With only this command it will not check for the loaded gmp/6.1.0 module in the $PATH variable instead it seems to only look for the systems /usr/bin i also created some extra setenv variables to set those at the loading of the module:
Here is an example module file
and the boost end part:
So I added those 2 Lines to the installation command:
cmake -DCMAKE_INSTALL_PREFIX:PATH=/software/octopus/0.7.4 -DGMP_INCLUDES=/software/gmp/6.1.0/include -DGMP_LIBRARIES=/software/gmp/6.1.0/lib ..After adding those commands cmake works mentioning the warning:
WARNING: Target "octopus" requests linking to directory "/software/gmp/6.1.0/lib". Targets may link only to libraries. CMake is dropping the item.make install then fails with:
I also tried boost modules in version 1.70 and 1.71 instead of the 1.65 needed coming to the same error.
2. Way desktop machine CentOS Linux release 7.9.2009 (Core)
As the installation you suggest starts with a git clone command I first load the module for it and some support stuff:
I know here curl is not in the PATH, but it was trust me. ;) So we set some prerequisite that we could satisfy
………(cuttet out the other stuff that worked)
I appreciate any help on this installation.
Regards, Hans