sobolevnrm
commented
2 years ago Thank you for the detailed report. What operating system is this?
Closed Shingzzz closed 2 years ago
sobolevnrm
commented
2 years ago Thank you for the detailed report. What operating system is this?
Shingzzz
commented
2 years ago Thank you for the detailed report. What operating system is this?
NAME="openEuler" VERSION="20.03 (LTS-SP3)" ID="openEuler" VERSION_ID="20.03" PRETTY_NAME="openEuler 20.03 (LTS-SP3)" ANSI_COLOR="0;31"
Linux version 4.19.90-2112.8.0.0131.oe1.aarch64
Shingzzz
commented
2 years ago hello , I try to install python3.6 , but there is a new problem:
-- Supplemental tools enabled
-- Building mesh
-- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem;apbs_routines
-- Building manip
-- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem;apbs_routines
CMake Error at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:146 (message):
Could NOT find Python3 (missing: Python3_LIBRARIES Python3_INCLUDE_DIRS
Development) (found suitable exact version "3.6.9")
Call Stack (most recent call first):
/usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:393 (_FPHSA_FAILURE_MESSAGE)
/usr/share/cmake/Modules/FindPython/Support.cmake:2261 (find_package_handle_standard_args)
/usr/share/cmake/Modules/FindPython3.cmake:300 (include)
tools/python/CMakeLists.txt:12 (find_package)It seems that I should install python3.6-devel , but I can only install python3.7-devel in this operating system , can I change the python version need for apbs ? and how to change ? please help me , thanks a lot .
alexreg
commented
2 years ago I got this issue too, except on macOS. The problem seems to be the EXACT parameter in the calls to find_package(Python3 ${PYTHON_VERSION} EXACT ..., which appear in the files CMakeLists.txt, tests/CMakeLists.txt, and tools/python/CMakeLists.txt. Removing the EXACT means it will find Python 3.6 or later, and the build seems to then succeed.
Edit: Alternatively, simply specifying -DPYTHON_VERSION=3.10 as an argument to the cmake command did the job for me. (Change to whatever Python 3.6+ version you have installed, and it should work.)
Shingzzz
commented
2 years ago I got this issue too, except on macOS. The problem seems to be the
EXACTparameter in the calls tofind_package(Python3 ${PYTHON_VERSION} EXACT ..., which appear in the filesCMakeLists.txt,tests/CMakeLists.txt, andtools/python/CMakeLists.txt. Removing theEXACTmeans it will find Python 3.6 or later, and the build seems to then succeed.Edit: Alternatively, simply specifying
-DPYTHON_VERSION=3.10as an argument to thecmakecommand did the job for me. (Change to whatever Python 3.6+ version you have installed, and it should work.)
thank you very much ! I solve this problem by your solution !
sobolevnrm
commented
2 years ago Thank you, @alexreg !
Shingzzz
commented
2 years ago I install apbs successfully , but when I run ctest -C Release --output-on-failure ，there are some mistakes:
83% tests passed, 3 tests failed out of 18
Total Test time (real) = 490.99 sec
The following tests FAILED:
16 - bem_test (Failed)
17 - bem-pKa_test (Failed)
18 - bem-binding-energy_test (Failed)
Errors while running CTestThere are some information：
16/18 Test #16: bem_test ..................................***Failed 1.24 sec
TESTING WITH BINARY_NAME:apbs
START_DIR:/root/zqc/apbs/build
--------------------------------------------------------------------------------
Testing input file 451c_order1.in
Computed result for index, 0, does not exist: list index out of rangeTest failed: list index out of range
Elapsed time: 0.915075 seconds
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Testing input file 451c_order5.in
Computed result for index, 0, does not exist: list index out of rangeTest failed: list index out of range
Elapsed time: 0.230859 seconds
--------------------------------------------------------------------------------
Total elapsed time: 1.145934 seconds
Test results have been logged
--------------------------------------------------------------------------------
Some tests failed: Number of test failures: 2
NOTE: Using apbs binary:/root/zqc/apbs/build/src/apbs
The following sections will be tested: bem
================================================================================
Running tests for bem section
BINARY: /root/zqc/apbs/build/src/apbs
INPUT: 451c_order1.in
COMMAND: ['/root/zqc/apbs/build/src/apbs', '451c_order1.in']
This executable compiled on Sep 28 2022 at 20:09:33
Parsing input file 451c_order1.in...
rank 0 size 1...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from test_proteins/451c.pqr.
terminate called after throwing an instance of 'std::invalid_argument'
what(): stoul
Checking for intermediate energies in input file 451c_order1.out
EXPECTED COMPUTED: 0
EXPECTED EXPECTED: 1
COMPUTED: []
EXPECTED: ['-4.678324477794E+03']
BINARY: /root/zqc/apbs/build/src/apbs
INPUT: 451c_order5.in
COMMAND: ['/root/zqc/apbs/build/src/apbs', '451c_order5.in']
17/18 Test #17: bem-pKa_test ..............................***Failed 0.79 sec
TESTING WITH BINARY_NAME:apbs
START_DIR:/root/zqc/apbs/build
--------------------------------------------------------------------------------
Testing input file ASH66.in
Computed result for index, 0, does not exist: list index out of rangeTest failed: list index out of range
Elapsed time: 0.210295 seconds
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Testing input file 2LZT-ASH66.in
Computed result for index, 0, does not exist: list index out of rangeTest failed: list index out of range
Elapsed time: 0.246886 seconds
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Testing input file 2LZT-noASH66.in
Computed result for index, 0, does not exist: list index out of rangeTest failed: list index out of range
Elapsed time: 0.241297 seconds
--------------------------------------------------------------------------------
Total elapsed time: 0.698478 seconds
Test results have been logged
--------------------------------------------------------------------------------
Some tests failed: Number of test failures: 3
NOTE: Using apbs binary:/root/zqc/apbs/build/src/apbs
The following sections will be tested: bem-pKa
================================================================================
Running tests for bem-pKa section
BINARY: /root/zqc/apbs/build/src/apbs
INPUT: ASH66.in
COMMAND: ['/root/zqc/apbs/build/src/apbs', 'ASH66.in']
This executable compiled on Sep 28 2022 at 20:09:33
Parsing input file ASH66.in...
rank 0 size 1...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from test_proteins/ASH66.pqr.
terminate called after throwing an instance of 'std::invalid_argument'
what(): stoul
Checking for intermediate energies in input file ASH66.out
EXPECTED COMPUTED: 0
EXPECTED EXPECTED: 1
COMPUTED: []
EXPECTED: ['-4.005763343995E+00']
BINARY: /root/zqc/apbs/build/src/apbs
INPUT: 2LZT-ASH66.in
COMMAND: ['/root/zqc/apbs/build/src/apbs', '2LZT-ASH66.in']
18/18 Test #18: bem-binding-energy_test ...................***Failed 0.71 sec
TESTING WITH BINARY_NAME:apbs
START_DIR:/root/zqc/apbs/build
--------------------------------------------------------------------------------
Testing input file 1d30.in
Computed result for index, 0, does not exist: list index out of rangeTest failed: list index out of range
Elapsed time: 0.2326 seconds
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Testing input file 1d30_monomer1.in
Computed result for index, 0, does not exist: list index out of rangeTest failed: list index out of range
Elapsed time: 0.197381 seconds
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Testing input file 1d30_monomer2.in
Computed result for index, 0, does not exist: list index out of rangeTest failed: list index out of range
Elapsed time: 0.184725 seconds
--------------------------------------------------------------------------------
Total elapsed time: 0.614706 seconds
Test results have been logged
--------------------------------------------------------------------------------
Some tests failed: Number of test failures: 3
NOTE: Using apbs binary:/root/zqc/apbs/build/src/apbs
The following sections will be tested: bem-binding-energy
================================================================================
Running tests for bem-binding-energy section
BINARY: /root/zqc/apbs/build/src/apbs
INPUT: 1d30.in
COMMAND: ['/root/zqc/apbs/build/src/apbs', '1d30.in']
This executable compiled on Sep 28 2022 at 20:09:33
Parsing input file 1d30.in...
rank 0 size 1...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from test_proteins/1d30.pqr.
terminate called after throwing an instance of 'std::invalid_argument'
what(): stoul
Checking for intermediate energies in input file 1d30.out
EXPECTED COMPUTED: 0
EXPECTED EXPECTED: 1
COMPUTED: []
EXPECTED: ['-2.197264516397E+04']
BINARY: /root/zqc/apbs/build/src/apbs
INPUT: 1d30_monomer1.in
COMMAND: ['/root/zqc/apbs/build/src/apbs', '1d30_monomer1.in']I have not modified apbs/examples file .
And when I run /usr/local/apbs/bin/tabipb 451c_order1.in
the result:
Segmentation fault (core dumped)
xiaopangjun666
commented
2 years ago Excuse me，how did you install UMFPACK? I can't find the UMFPACK package with error when installing
Shingzzz
commented
2 years ago Excuse me，how did you install UMFPACK? I can't find the UMFPACK package with error when installing
you can install intel blas or suitesparse (and its devel) , and vim /etc/profile set LD_LIBRARY_PATH=(your install path):$LD_LIBRARY_PATH
xiaopangjun666
commented
2 years ago Thank you very much！I find suitesparse in /usr/lib64 and set the LD_LIBRARY_PATH=/usr/lib64/:$LD_LIBRARY_PATH,but error when i try cmake again.could you tell me the reason,please
Shingzzz
commented
2 years ago Thank you very much！I find suitesparse in /usr/lib64 and set the LD_LIBRARY_PATH=/usr/lib64/:$LD_LIBRARY_PATH,but error when i try cmake again.could you tell me the reason,please
did you source /etc/profile ? or , you can try to install suitesparse-devel and try to cmake again .
and you can echo $LD_LIBRARY_PATH , be sure that /usr/lib64 in it.
Describe the bug hello guys, I would like to install apbs 3.4.1 from source code , but I met a lot of errors , I try to solve a little of them , such as dependencies and environmental path . There is a error that I think I can`t solve.
do I have to use python3.6 ? I can`t change the python version casually .
To Reproduce Steps to reproduce the behavior:
Context
By the way , could you don`t close this issue until I install apbs successfully ? Thank u very much .😭