Function to find the atoms of a given mask that appear in a region of xyz coordinate space? about pytraj HOT 10 CLOSED

Would this be a useful function in pytraj? If so, should I just clone the repo and make a PR?

Dear @sastrys1, feel free to make a PR. I will be happy to review it. Thanks.

Thanks for this tool, I really love using pytraj!!

Sweet. I am glad that pytraj is useful. Cheers.

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@hainm Do you have any advice on how to run pytraj with the changes I've made and then run the test code? I'm not able to build pytraj using the python setup.py install command because the libcpptraj installation is failing. Do I need to be able to build the entire thing to test changes?

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Do I need to be able to build the entire thing to test changes?

yeah, I think so. Otherwise, you can update the source code in the install path directly and make a PR here for CI to test.

because the libcpptraj installation is failing.

what's the error?

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This is the error:

Error: LAPACK/BLAS build/link failed: g++ -Wall -fopenmp -O3 -fPIC -std=gnu++11 -o testp testp.cpp -L/gstore/apps/imkl/2021.4.0/mkl/2021.4.0/lib/intel64/lib -llapack -L/gstore/apps/imkl/2021.4.0/mkl/2021.4.0/lib/intel64/lib -lblas -lgfortran -lpthread -fopenmp
Error: Error message follows:
Error: /gstore/apps/binutils/2.37-GCCcore-11.2.0/bin/ld.gold: error: cannot find -llapack
/gstore/apps/binutils/2.37-GCCcore-11.2.0/bin/ld.gold: error: cannot find -lblas
/local/tmp/ccQzyy18.o:testp.cpp:function main: error: undefined reference to 'dsyev_'
/local/tmp/ccQzyy18.o:testp.cpp:function main: error: undefined reference to 'dgemm_'
collect2: error: ld returned 1 exit status
Traceback (most recent call last):
File "/gstore/scratch/u/sastrys1/pytraj/scripts/install_libcpptraj.py", line 225, in
install_libcpptraj(compiler, build_flag, args.j)
File "/gstore/scratch/u/sastrys1/pytraj/scripts/install_libcpptraj.py", line 173, in install_libcpptraj
subprocess.check_call(cm, shell=True)
File "/gstore/apps/Python/3.9.6-GCCcore-11.2.0/lib/python3.9/subprocess.py", line 373, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'bash configure --requires-flink -shared -noarpack --with-blas=/gstore/apps/imkl/2021.4.0/mkl/2021.4.0/lib/intel64 --with-lapack=/gstore/apps/imkl/2021.4.0/mkl/2021.4.0/lib/intel64 --with-bzlib=/gstore/apps/Python/3.9.6-GCCcore-11.2.0 --with-zlib=/gstore/apps/Python/3.9.6-GCCcore-11.2.0 -amberlib -openmp -nosanderlib gnu' returned non-zero exit status 1.

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thanks @sastrys1 for the report.
FYI that here is how we build libcpptraj and pytraj in github action:

List of dependency:

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Decided to just make direct changes to my conda pytraj repo and test them, and then commit them. Does simply pushing to my forked repo trigger a travis build?

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Made a PR. Thanks for the help.

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Thanks. Let's move our discussion to there #1641 then.

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oh, for the record:

you can copy the existing libcpptraj.so{dylib} from the installed pytraj to $CPPTRAJHOME/lib (CPPTRAJHOME points to source folder of cpptraj). Doing this way you don't need to rebuild cpptraj. (pytraj only needs libcpptraj and the header files (.h)).

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