Installation HHblits on HPC

[merytouceda]

Hi! I am trying to install the dependencies of AGNOSTOS following your instructions here: https://github.com/functional-dark-side/agnostos-wf/blob/master/AGNOSTOS_usage.md

And everything seems to be working! Yay! (thanks for that). Except HHblits.

When running make -j 8 and make install I get the following error:

I tried a couple of times, to try to make sure I didn't make a mistake, but I got the same thing. Do you think it has to do with my permissions in the hpc?

Best,

Mery

[ChiaraVanni]

Hi @merytouceda, did you manage to solve this?

Chiara

[merytouceda]

Hi!

I haven't yet :(

Mery

El jue., 24 feb. 2022 2:56, Chiara Vanni @.***> escribió:

Hi @merytouceda https://github.com/merytouceda, did you manage to solve this?

Chiara

— Reply to this email directly, view it on GitHub https://github.com/functional-dark-side/agnostos-wf/issues/12#issuecomment-1049679078, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHD2U3FCKDQ2ZBOWMPB5D5DU4X6D3ANCNFSM5OFGI2BA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you were mentioned.Message ID: @.***>

[ChiaraVanni]

Hi! Can you send the full log of the hhblits installation?

Chiara

[merytouceda]

This is it:

(puma) (base) @. build]$ cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX=/groups/egornish/software/agnostos-wf/bin/hh-suite .. -- Compiler is GNU -- Found OpenMP -- Configuring done -- Generating done -- Build files have been written to: /groups/egornish/software/agnostos-wf/programs/hh-suite/build (puma) (base) @. build]$ make -j 8 [ 7%] [ 7%] [ 7%] Built target generated Built target ffindex Built target A3M_COMPRESS [ 17%] [ 18%] Built target CS_OBJECTS [ 19%] Built target hhviterbialgorithm_with_celloff_and_ss [ 21%] [ 23%] [ 23%] [ 25%] Built target hhviterbialgorithm_and_ss Built target hhviterbialgorithm_with_celloff Built target mpq [ 26%] Built target ffindex_apply Built target ffindex_build Built target ffindex_from_fasta [ 27%] [ 28%] [ 30%] [ 31%] [ 32%] [ 34%] Built target ffindex_from_fasta_with_split Built target ffindex_get [ 35%] Built target ffindex_modify Built target ffindex_order Built target ffindex_reduce Built target ffindex_unpack Built target a3m_database_extract [ 60%] Built target a3m_database_filter [ 63%] Built target a3m_database_reduce [ 65%] [ 67%] Built target a3m_extract Built target a3m_reduce [ 78%] Built target ffindex_apply_mpi [ 80%] Built target HH_OBJECTS Linking CXX executable cstranslate_mpi Linking CXX executable hhalign_mpi [ 81%] [ 82%] Linking CXX executable hhblits_mpi [ 84%] [ 85%] Built target cstranslate [ 86%] Built target hhalign Built target hhalign_omp Built target hhblits Built target hhblits_ca3m Scanning dependencies of target hhsearch [ 88%] [ 89%] [ 90%] [ 92%] Built target hhblits_omp Built target hhmake Built target hhconsensus Built target hhfilter /opt/ohpc/pub/mpi/openmpi3-gnu8/3.1.4/lib/libmpi_cxx.so: undefined reference to @._1.3.8' /opt/ohpc/pub/mpi/openmpi3-gnu8/3.1.4/lib/libmpi_cxx.so: undefined reference to `operator delete(void, unsigned **@._1.3.9' collect2: error: ld returned 1 exit status make[2]: [src/cstranslate_mpi] Error 1 make[1]: [src/CMakeFiles/cstranslate_mpi.dir/all] Error 2 make[1]: Waiting for unfinished jobs.... Scanning dependencies of target hhsearch_mpi /opt/ohpc/pub/mpi/openmpi3-gnu8/3.1.4/lib/libmpi_cxx.so: undefined reference to @._1.3.8' /opt/ohpc/pub/mpi/openmpi3-gnu8/3.1.4/lib/libmpi_cxx.so: undefined reference to `operator delete(void, unsigned **@._1.3.9' collect2: error: ld returned 1 exit status make[2]: [src/hhblits_mpi] Error 1 make[1]: [src/CMakeFiles/hhblits_mpi.dir/all] Error 2 /opt/ohpc/pub/mpi/openmpi3-gnu8/3.1.4/lib/libmpi_cxx.so: undefined reference to @._1.3.8' /opt/ohpc/pub/mpi/openmpi3-gnu8/3.1.4/lib/libmpi_cxx.so: undefined reference to operator delete(void*, unsigned ***@***.***_1.3.9' collect2: error: ld returned 1 exit status make[2]: *** [src/hhalign_mpi] Error 1 make[1]: *** [src/CMakeFiles/hhalign_mpi.dir/all] Error 2 [ 93%] Building CXX object src/CMakeFiles/hhsearch.dir/hhblits_app.cpp.o [ 94%] Building CXX object src/CMakeFiles/hhsearch_mpi.dir/hhblits_mpi.cpp.o Linking CXX executable hhsearch [ 94%] Built target hhsearch Linking CXX executable hhsearch_mpi /opt/ohpc/pub/mpi/openmpi3-gnu8/3.1.4/lib/libmpi_cxx.so: undefined reference to ***@***.***_1.3.8' /opt/ohpc/pub/mpi/openmpi3-gnu8/3.1.4/lib/libmpi_cxx.so: undefined reference tooperator delete(void*, unsigned @._1.3.9' collect2: error: ld returned 1 exit status make[2]: [src/hhsearch_mpi] Error 1 make[1]: [src/CMakeFiles/hhsearch_mpi.dir/all] Error 2 make: [all] Error 2

Could it be associated with the fact that I don’t have a "-DCMAKE_INSTALL_PREFIX=/groups/egornish/software/agnostos-wf/bin/hh-suite” that directory? My hh-suite directory is not in the bin, is in programs. Is that a mistake in the installation script?

Mery

María Touceda Suárez Graduate Research Associate Barberán Lab Department of Environmental Science, University of Arizona

@.*** Pronouns: She/Her/Hers barberanalbert.wixsite.com/labpage/people

On Feb 24, 2022, at 7:11 AM, Chiara Vanni @.***> wrote:

Hi! Can you send the full log of the hhblits installation?

Chiara

— Reply to this email directly, view it on GitHub https://github.com/functional-dark-side/agnostos-wf/issues/12#issuecomment-1049899357, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHD2U3G7RL7LWSDS564H4TTU4Y4CPANCNFSM5OFGI2BA. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you were mentioned.