pyscf/gpu4pyscf

Unable to compile in Docker image

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#126 opened on Mar 20, 2024

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Description

Hi,

I cannot get gpu4pyscf to compile inside the environment generated through 'dockerfiles/compile/Dockerfile'

Environment:

uname -a:
Linux 6.5.0-25-generic #25~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 20 16:09:15 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
nvidia-smi:
+---------------------------------------------------------------------------------------+
| NVIDIA-SMI 535.161.07             Driver Version: 535.161.07   CUDA Version: 12.2     |
|-----------------------------------------+----------------------+----------------------+
| GPU  Name                 Persistence-M | Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp   Perf          Pwr:Usage/Cap |         Memory-Usage | GPU-Util  Compute M. |
|                                         |                      |               MIG M. |
|=========================================+======================+======================|
|   0  NVIDIA GeForce GTX 1080 Ti     Off | 00000000:01:00.0  On |                  N/A |
| 30%   60C    P2             175W / 275W |   5021MiB / 11264MiB |    100%      Default |
|                                         |                      |                  N/A |
+-----------------------------------------+----------------------+----------------------+

Issues:

  1. unclear instructions on getting started

Based on assumptions / trail and error I followed this scenario:

  • build docker
  • login to docker env on a terminal
  • put gpu4pyscf inside '/usr/local/lib/python3.9/dist-packages/pyscf/'
  • CD into gpu4pyscf
  • run 'sh build.sh'

=> Are these steps correct? Or am I missing something already?

I suggest to add some instructions to get started with compiling to the Readme file

  1. compile failed due to missing Fortran compiler - no fortran compiler found in docker env

Actions taken: apt-get update && apt-get install gfortran

=> is this the correct Fortran compiler?

I Suggest to add proper Fortran compiler to docker 'compile' environment or add instructions for selecting/installing the correct compiler

  1. compile failed due to undefined references:

Errors below, I currently haven't been able to find out what I am missing.

Scanning dependencies of target multicharge-exe
[ 65%] Building Fortran object _deps/multicharge-build/app/CMakeFiles/multicharge-exe.dir/main.f90.o
[ 67%] Linking Fortran executable multicharge
/usr/bin/ld: ../libmulticharge.a(blas.F90.o): in function `__multicharge_blas_MOD_mchrg_dgemm':
/usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/blas.F90:520: undefined reference to `dgemm_'
/usr/bin/ld: ../libmulticharge.a(blas.F90.o): in function `__multicharge_blas_MOD_mchrg_sgemm':
/usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/blas.F90:475: undefined reference to `sgemm_'
/usr/bin/ld: ../libmulticharge.a(blas.F90.o): in function `__multicharge_blas_MOD_mchrg_dsymv':
/usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/blas.F90:430: undefined reference to `dsymv_'
/usr/bin/ld: ../libmulticharge.a(blas.F90.o): in function `__multicharge_blas_MOD_mchrg_ssymv':
/usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/blas.F90:397: undefined reference to `ssymv_'
/usr/bin/ld: ../libmulticharge.a(blas.F90.o): in function `__multicharge_blas_MOD_mchrg_dgemv':
/usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/blas.F90:364: undefined reference to `dgemv_'
/usr/bin/ld: ../libmulticharge.a(blas.F90.o): in function `__multicharge_blas_MOD_mchrg_sgemv':
/usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/blas.F90:330: undefined reference to `sgemv_'
/usr/bin/ld: ../libmulticharge.a(lapack.F90.o): in function `__multicharge_lapack_MOD_mchrg_dsytri':
/usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/lapack.F90:353: undefined reference to `dsytri_'
/usr/bin/ld: /usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/lapack.F90:353: undefined reference to `dsytri_'
/usr/bin/ld: /usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/lapack.F90:353: undefined reference to `dsytri_'
/usr/bin/ld: ../libmulticharge.a(lapack.F90.o): in function `__multicharge_lapack_MOD_mchrg_ssytri':
/usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/lapack.F90:322: undefined reference to `ssytri_'
/usr/bin/ld: /usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/lapack.F90:322: undefined reference to `ssytri_'
/usr/bin/ld: /usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/lapack.F90:322: undefined reference to `ssytri_'
/usr/bin/ld: ../libmulticharge.a(lapack.F90.o): in function `__multicharge_lapack_MOD_mchrg_dsytrs':
/usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/lapack.F90:247: undefined reference to `dsytrs_'
/usr/bin/ld: ../libmulticharge.a(lapack.F90.o): in function `__multicharge_lapack_MOD_mchrg_ssytrs':
/usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/lapack.F90:221: undefined reference to `ssytrs_'
/usr/bin/ld: ../libmulticharge.a(lapack.F90.o): in function `__multicharge_lapack_MOD_mchrg_dsytrf':
/usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/lapack.F90:183: undefined reference to `dsytrf_'
/usr/bin/ld: /usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/lapack.F90:190: undefined reference to `dsytrf_'
/usr/bin/ld: /usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/lapack.F90:183: undefined reference to `dsytrf_'
/usr/bin/ld: /usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/lapack.F90:190: undefined reference to `dsytrf_'
/usr/bin/ld: /usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/lapack.F90:183: undefined reference to `dsytrf_'
/usr/bin/ld: ../libmulticharge.a(lapack.F90.o):/usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/lapack.F90:183: more undefined references to `dsytrf_' follow
/usr/bin/ld: ../libmulticharge.a(lapack.F90.o): in function `__multicharge_lapack_MOD_mchrg_ssytrf':
/usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/lapack.F90:144: undefined reference to `ssytrf_'
/usr/bin/ld: /usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/lapack.F90:151: undefined reference to `ssytrf_'
/usr/bin/ld: /usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/lapack.F90:144: undefined reference to `ssytrf_'
/usr/bin/ld: /usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/lapack.F90:151: undefined reference to `ssytrf_'
/usr/bin/ld: /usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/lapack.F90:144: undefined reference to `ssytrf_'
/usr/bin/ld: ../libmulticharge.a(lapack.F90.o):/usr/local/lib/python3.9/dist-packages/pyscf/gpu4pyscf/build/temp.linux-x86_64/gpu4pyscf/deps/src/dftd4_static-build/_deps/multicharge-src/src/multicharge/lapack.F90:144: more undefined references to `ssytrf_' follow
collect2: error: ld returned 1 exit status
gmake[5]: *** [_deps/multicharge-build/app/CMakeFiles/multicharge-exe.dir/build.make:105: _deps/multicharge-build/app/multicharge] Error 1
gmake[4]: *** [CMakeFiles/Makefile2:489: _deps/multicharge-build/app/CMakeFiles/multicharge-exe.dir/all] Error 2
gmake[3]: *** [Makefile:160: all] Error 2
gmake[2]: *** [CMakeFiles/dftd4_static.dir/build.make:130: deps/src/dftd4_static-stamp/dftd4_static-build] Error 2
gmake[1]: *** [CMakeFiles/Makefile2:211: CMakeFiles/dftd4_static.dir/all] Error 2
gmake: *** [Makefile:103: all] Error 2

Contributor guide

Research direction
Investigate why BLAS/LAPACK libraries are missing or not linked during CMake build in Docker image; check if libblas dev and liblapack dev are installed, and ensure CMake finds them.
Tech stack
docker
Domain
backenddevops
Issue type
Bug
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
2
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
Half day
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Active
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Needs investigation
Prerequisites
GitDocker
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
30