install fail on Ubuntu 22.x: No module named boost_python_meta_ext

[iqphan]

Hello,

I work for a govt-funded project and as a contract requirement must install this software.

Back in 2014 when I last installed it on Ubuntu, the install threw the same error "No module named boost_python_meta_ext". At the time, this was solved by installing boost separately.

After the first attempt at installation failed, I installed boost with:

1. sudo apt install libboost-all-dev => MolProbity installation fails again with "No module named boost_python_meta_ext".
2. install boost from boost.org source distro => no change, MolProbity installation fails again with "No module named boost_python_meta_ext".

Boost installation is perhaps not the issue, searching hints at ccp4 or phenix issues...maybe?? there's no ccp4 or phenix installed on that machine, they are not listed as a requirement.

OS: Ubuntu 22.04
MolProbity: git clone from this repo
Command: bash ./install_via_bootstrap.sh 2
Error:

In file included from /usr/include/pthread.h:33,
from /usr/include/x86_64-linux-gnu/c++/11/bits/gthr-default.h:35,
from /usr/include/x86_64-linux-gnu/c++/11/bits/gthr.h:148,
from /usr/include/c++/11/ext/atomicity.h:35,
from /usr/include/c++/11/bits/basic_string.h:39,
from /usr/include/c++/11/string:55,
from /home/ubuntu/Downloads/MolProbity/modules/boost/boost/thread/exceptions.hpp:20,
from /home/ubuntu/Downloads/MolProbity/modules/boost/boost/thread/pthread/thread_data.hpp:10,
from /home/ubuntu/Downloads/MolProbity/modules/boost/boost/thread/thread_only.hpp:17,
from /home/ubuntu/Downloads/MolProbity/modules/boost/libs/thread/src/pthread/thread.cpp:11:
/home/ubuntu/Downloads/MolProbity/modules/boost/boost/thread/pthread/thread_data.hpp:60:5: error: missing binary operator before token "("
60 | #if PTHREAD_STACK_MIN > 0
| ^~~~~~~~~~~~~~~~~
scons: *** [boost/libs/thread/src/pthread/thread.o] Error 1
scons: building terminated because of errors.
usr+sys time: 1.89 seconds
wall clock time: 45.42 seconds
Process failed with return code 2
Traceback (most recent call last):
File "modules/chem_data/cablam_data/rebuild_cablam_cache.py", line 8, in
from mmtbx.rotamer.n_dim_table import NDimTable
File "/home/ubuntu/Downloads/MolProbity/modules/cctbx_project/mmtbx/rotamer/n_dim_table.py", line 2, in
from scitbx.array_family import flex
File "/home/ubuntu/Downloads/MolProbity/modules/cctbx_project/scitbx/array_family/flex.py", line 7, in
import boost_adaptbx.boost.optional # import dependency
File "/home/ubuntu/Downloads/MolProbity/modules/cctbx_project/boost_adaptbx/boost/optional.py", line 2, in
import boost_adaptbx.boost.python as bp
File "/home/ubuntu/Downloads/MolProbity/modules/cctbx_project/boost_adaptbx/boost/python.py", line 40, in
ext = import_ext("boost_python_meta_ext")
File "/home/ubuntu/Downloads/MolProbity/modules/cctbx_project/boost_adaptbx/boost/python.py", line 33, in import_ext
+ [" "+p for p in sys.path]))
ImportError: import("boost_python_meta_ext"): No module named boost_python_meta_ext

[iqphan]

FYI I modified the boost thread_data.hpp as discribed in this post: boostorg/thread#364 (comment)

Restarting install_via_bootstrap.sh failed with the error directory already exists, use --force.

Restarting install_via_bootstrap.sh --force has zero effect, I still got the error directory already exists, use --force :(

So I did a 'commit -a' from inside modules/boost/boost and ran:
./conda_base/bin/python2.7 bootstrap.py --builder=molprobity --use-conda 2
It failed with:

g++ -o boost_adaptbx/tests/tst_optional_copy -s -pthread boost_adaptbx/tests/tst_optional_copy.o -Llib -L/home/ubuntu/Downloads/MolProbity/modules/lib -L/home/ubuntu/Downloads/MolProbity/modules/cctbx_project/lib -L/home/ubuntu/Downloads/MolProbity/conda_base/lib -Llib -L/home/ubuntu/Downloads/MolProbity/modules/lib -L/home/ubuntu/Downloads/MolProbity/modules/cctbx_project/lib -lboost_thread -lboost_system
/usr/bin/ld: boost_adaptbx/tests/tst_optional_copy.o: in function void boost_adaptbx::tst_optional_copy::exercise<std::vector<int, std::allocator<int> > >(std::vector<int, std::allocator<int> > const&, std::vector<int, std::allocator<int> > const&, bool)': tst_optional_copy.cpp.text.ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b[_ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b]+0x5a6): undefined reference to std::_throw_bad_array_new_length()'
/usr/bin/ld: tst_optional_copy.cpp.text.ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b[_ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b]+0x5ce): undefined reference to std::_throw_bad_array_new_length()' /usr/bin/ld: tst_optional_copy.cpp.text.ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b[_ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b]+0x5de): undefined reference to std::_throw_bad_array_new_length()'
/usr/bin/ld: tst_optional_copy.cpp.text.ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b[_ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b]+0x5ee): undefined reference to std::_throw_bad_array_new_length()' /usr/bin/ld: tst_optional_copy.cpp.text.ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b[_ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b]+0x5fe): undefined reference to std::_throw_bad_array_new_length()'
/usr/bin/ld: boost_adaptbx/tests/tst_optional_copy.o:tst_optional_copy.cpp.text.ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b[_ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b]+0x616): more undefined references to `std::_throw_bad_array_new_length()' follow
collect2: error: ld returned 1 exit status
scons: *** [boost_adaptbx/tests/tst_optional_copy] Error 1
scons: building terminated because of errors.

Please do you have a binary of molscript that runs on Ubuntu?

[chrissciwilliams]

Sorry for this difficulty. It's unlikely to be the problem, but I want to make sure that the command is well-formed. The "2" actually goes with a "--nproc=" flag, like so: ./conda_base/bin/python2.7 bootstrap.py --builder=molprobity --use-conda *--nproc=*2 You can try applying the --force flag here. ./conda_base/bin/python2.7 bootstrap.py --builder=molprobity --use-conda *--nproc=*2 --force (The install_via_boostrap.py script is trying to make things easy by managing all the flags for you, but that means it doesn't really accept new flags.)

…

-Christopher Williams ---Richardson Lab, Duke University

On Mon, Nov 7, 2022 at 6:18 PM iqphan ***@***.***> wrote: FYI I modified the boost thread_data.hpp as discribed in this post: boostorg/thread#364 (comment) <boostorg/thread#364 (comment)> Restarting install_via_bootstrap.sh failed with the error directory already exists, use --force. Restarting install_via_bootstrap.sh --force has zero effect, I still got the error directory already exists, use --force :( So I did a 'commit -a' from inside modules/boost/boost and ran: ./conda_base/bin/python2.7 bootstrap.py --builder=molprobity --use-conda 2 It failed with: g++ -o boost_adaptbx/tests/tst_optional_copy -s -pthread boost_adaptbx/tests/tst_optional_copy.o -Llib -L/home/ubuntu/Downloads/MolProbity/modules/lib -L/home/ubuntu/Downloads/MolProbity/modules/cctbx_project/lib -L/home/ubuntu/Downloads/MolProbity/conda_base/lib -Llib -L/home/ubuntu/Downloads/MolProbity/modules/lib -L/home/ubuntu/Downloads/MolProbity/modules/cctbx_project/lib -lboost_thread -lboost_system /usr/bin/ld: boost_adaptbx/tests/tst_optional_copy.o: in function void boost_adaptbx::tst_optional_copy::exercise<std::vector<int, std::allocator<int> > >(std::vector<int, std::allocator<int> > const&, std::vector<int, std::allocator<int> > const&, bool)': tst_optional_copy.cpp.text.ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b[_ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b]+0x5a6): undefined reference to std::_throw_bad_array_new_length()' /usr/bin/ld: tst_optional_copy.cpp.text.ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b[_ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b]+0x5ce): undefined reference to std::_throw_bad_array_new_length()' /usr/bin/ld: tst_optional_copy.cpp.text.ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b[_ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b]+0x5de): undefined reference to std::_throw_bad_array_new_length()' /usr/bin/ld: tst_optional_copy.cpp.text.ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b[_ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b]+0x5ee): undefined reference to std::_throw_bad_array_new_length()' /usr/bin/ld: tst_optional_copy.cpp.text.ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b[_ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b]+0x5fe): undefined reference to std::_throw_bad_array_new_length()' /usr/bin/ld: boost_adaptbx/tests/tst_optional_copy.o:tst_optional_copy.cpp.text.ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b[_ZN13boost_adaptbx17tst_optional_copy8exerciseISt6vectorIiSaIiEEEEvRKT_S7_b]+0x616): more undefined references to `std::_throw_bad_array_new_length()' follow collect2: error: ld returned 1 exit status scons: *** [boost_adaptbx/tests/tst_optional_copy] Error 1 scons: building terminated because of errors. Please do you have a binary of molscript that runs on Ubuntu? — Reply to this email directly, view it on GitHub <#24 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACLEREHZ7WWWRFHIKW2QHITWHGE3FANCNFSM6AAAAAARZVNIXI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[iqphan]

Thank you for the suggestion. This is odd, I am now getting:

SCons Error: option -j: invalid integer value: '--nproc=2'

[chrissciwilliams]

That is indeed odd.

It looks like my text formatting has not translated from my email to GitHub. Without formatting, it should look like:
python bootstrap.py --builder=molprobity --use-conda --nproc=2

It looks like the entire "--nproc=2" is being passed to scons, rather than just the "2". I can reproduce this if I try the command:
python bootstrap.py --builder=molprobity --use-conda --nproc=--nproc=2 build

Something like this will get run if you try: "python install_via_bootstrap.py --nproc=2"

bootstrap.py and install_via_bootstrap.py are not the same thing and they take different arguments.
bootstrap.py accepts many arguments, including --nproc=#
install_via_bootstrap.py accepts only a single argument, an integer, which it then uses to construct a --nproc=# flag for its internal invocation of bootstrap.py

Allocating additional processors to the build process in convenient, but not necessary. Perhaps we should skip that step for now.

[iqphan]

Sorry I am now completely confused. I ran:

./conda_base/bin/python2.7 bootstrap.py --builder=molprobity --use-conda --nproc=2 --force

I cannot find install_via_bootstrap.py , only the install_via_bootstrap.sh shell script

[iqphan]

Please can you close this thread and switch to: #25 ?