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From: | Shawn |
Subject: | [ESPResSo-users] 回复: 回复: 回复: 回复: Problem with installation of espresso-4.1.0 |
Date: | Fri, 4 Oct 2019 11:27:22 -0500 |
Hi JN, I just tried to use another version of gcc (6.3.1), the result seemed better. But I got an error similar to I posted in July: [ 58%] Generating code_info.pyx Fatal Python error: Py_Initialize: can't initialize sys standard streams Traceback (most recent call last): File "/home/zhsh/sourcecode/espresso410/espresso/src/python/espressomd/io/__init__.py", line 17, in <module> File "/home/zhsh/sourcecode/espresso410/espresso/src/python/espressomd/io/writer/__init__.py", line 17, in <module> ValueError: attempted relative import beyond top-level package /bin/sh: line 1: 72159 Aborted (core dumped) /home/zhsh/soft/python3/bin/python3 gen_code_info.py /home/zhsh/sourcecode/espresso410/espresso/src/config/features.def /home/zhsh/sourcecode/espresso410/espresso/build/src/python/espressomd/code_info.pyx make[2]: *** [src/python/espressomd/code_info.pyx] Error 134 make[1]: *** [src/python/espressomd/CMakeFiles/espressomd_code_info.dir/all] Error 2 make: *** [all] Error 2 and the patch file you uploaded before doesn’t work now. Could you help me to fix this problem? Thank you very much. Best, Shawn 发件人: Jean-Noël Grad Hi, I'm using cmake 3.10.2 on Ubuntu 18.04 and cmake 3.14.6 on CentOS 7 with devtoolset 6. Your FFTW3 error is reproducible on CentOS 7 by doing this: "cmake ..; mv /usr/include/fftw3.h /usr/include/fftw3.h.bak; make -j12". Not sure why in your environment cmake detects fftw3.h but not your compiler. Maybe try this: locate the path to the FFTW3 header file with command 'find /usr/include -name "fftw3.h"', you should get something like /usr/include/fftw3.h, then only provide the directory name as an include path for your compiler with 'cmake .. -DCMAKE_CXX_FLAGS="-isystem /usr/include/"'. It works on my CentOS 7 when I have FFTW3 installed in another place than the standard /usr/include/fftw3.h (CMake will complain it can't find FFTW3, but the compiler directly gets the path so compilation works). Best, JN On 10/4/19 12:18 AM, Shawn wrote: > Hi JN, > > After I updated gcc, the Cmake returned a “0” code with the command line > “echo $?” and I didn’t use your patch when I tried to install > espresso-4.1.0. As you mentioned, it might be my espresso directory was > not clean. So I deleted the whole directory, unpacked the package and > rebuilt it again. But error was still there, fftw3.h isn't found. > > Anyway, thanks very much JN, and I really appreciate your help. Could > you tell me which version of cmake you use? > > Best, > > Shawn > > *发件人: *Jean-Noël Grad <mailto:address@hidden> > *发送时间: *2019年10月3日16:25 > *收件人: *address@hidden <mailto:address@hidden> > *主题: *Re: [ESPResSo-users] 回复: 回复: Problem with installation of > espresso-4.1.0 > > Hi Shawn, > > You won't be able to compile espresso if CMake returns a non-zero error > > code. You can show the error code with the command line "echo $?", once > > the "cmake .." command has completed ($? is a variable that stores the > > error code of the previous command). I do not understand how you were > > able to run the compiler when CMake failed: when I reproduce your CMake > > error message by renaming the src/python/espressomd/io directory to > > src/python/espressomd/io_, the command "make -j12" fails because the > > Makefile runs CMake first, sees the error code is 1, and stops. > > If you renamed the io directory using my patch from July, please know it > > isn't necessary anymore. We found out the source of the issue with > > Python standard streams is caused by a malformed export command in the > > "${HOME}/.bashrc" file. You can find the explanation and a clean > > solution here: > > https://github.com/espressomd/espresso/issues/3149#issuecomment-529974793 > > I'm not sure why fftw3.h isn't found by the compiler given CMake found > > it. It could be that you ran "cmake .." in a build directory that still > > contained files from a previous build. I has never been an issue for us, > > but apparently your CMake program doesn't seem to correctly overwrite > > old files. It could be a good idea to always clean your build directory > > before attempting a new build. You probably also should replace the > > content of /home/zhsh/sourcecode/espresso410/espresso by a fresh copy of > > the espresso source code, because src/python/espressomd/io is now either > > renamed or missing. > > Best, > > JN > > On 10/3/19 10:15 PM, Shawn wrote: > >> Hi JN, > >> Thanks for your help. I've updated my gcc to version 7.3.1 and I can > >> pass the configuring process. But I got a new error below: > >> > >> [ 50%] Building CXX object > >> src/core/cluster_analysis/CMakeFiles/cluster_analysis.dir/ClusterStructure.cpp.o > >> In file included from > >> /home/zhsh/sourcecode/espresso410/espresso/src/core/electrostatics_magnetostatics/p3m.hpp:58:0, > >> from > >> /home/zhsh/sourcecode/espresso410/espresso/src/core/electrostatics_magnetostatics/coulomb_inline.hpp:32, > >> from > >> /home/zhsh/sourcecode/espresso410/espresso/src/core/bonded_interactions/bonded_coulomb_sr.hpp:36, > >> from > >> /home/zhsh/sourcecode/espresso410/espresso/src/core/energy_inline.hpp:61, > >> from > >> /home/zhsh/sourcecode/espresso410/espresso/src/core/pair_criteria/pair_criteria.hpp:22, > >> from > >> /home/zhsh/sourcecode/espresso410/espresso/src/core/cluster_analysis/ClusterStructure.hpp:23, > >> from > >> /home/zhsh/sourcecode/espresso410/espresso/src/core/cluster_analysis/ClusterStructure.cpp:19: > >> /home/zhsh/sourcecode/espresso410/espresso/src/core/electrostatics_magnetostatics/fft.hpp:51:10: > >> fatal error: fftw3.h: No such file or directory > >> #include <fftw3.h> > >> ^~~~~~~~~ > >> compilation terminated. > >> make[2]: *** > >> [src/core/cluster_analysis/CMakeFiles/cluster_analysis.dir/ClusterStructure.cpp.o] > >> Error 1 > >> make[1]: *** > >> [src/core/cluster_analysis/CMakeFiles/cluster_analysis.dir/all] Error 2 > >> make: *** [all] Error 2 > >> > >> It seems that there's something wrong with my fftw library. But I can > >> install espresso-4.0.2 with fftw successfully. Do you have any > >> suggestions for solving this problem? > >> Attached please find the output of cmake. > >> > >> Best, > >> Shawn > >> > >> Jean-Noël Grad <address@hidden > >> <mailto:address@hidden>> 于2019年10月3日周四 下午12:06写道: > >> > >> Hi Shawn, > >> > >> I just tried compiling espresso 4.1 on CentOS 7 with CMake 3.14.6 > >> with a > >> C++ standard not recognized by my gcc v6.3.1 and CMake did throw a long > >> list of errors messages: "Target ... requires the language dialect > >> CXX.. > >> but CMake does not know the compile flags to use to enable it". The > >> return code is 1. I can't figure out why your version of CMake doesn't > >> show that error nor display the compiler name and version. > >> > >> In any case, you'll need to install a newer version of gcc, version > >> 4.9.0 or later, to compile espresso 4.1. > >> > >> Best, > >> JN > >> > >> On 10/3/19 6:18 PM, Shawn wrote: > >> > Hi JN, > >> > > >> > My gcc version is 4.8.5, and my cmake version is 3.14.5. So I should > >> > update my gcc to newer version? > >> > > >> > Regards, > >> > > >> > Shawn > >> > > >> > *发件人: *Jean-Noël Grad <mailto:address@hidden > >> <mailto:address@hidden>> > >> > *发送时间: *2019年10月3日11:11 > >> > *收件人: *address@hidden > >> <mailto:address@hidden> > >> <mailto:address@hidden > >> <mailto:address@hidden>> > >> > *主题: *Re: [ESPResSo-users] 回复: Problem with installation of > >> > espresso-4.1.0 > >> > > >> > Hi Shawn, > >> > > >> > It looks like your compiler doesn't know the C++14 standard. For > >> example: > >> > > >> > > /home/zhsh/sourcecode/espresso/src/utils/include/utils/Vector.hpp: > >> > > >> > > error: parameter declared ‘auto’ > >> > > >> > > [](auto ai, auto bi) { return ai * bi; }); > >> > > >> > > ^ > >> > > >> > > error: parameter declared ‘auto’ > >> > > >> > > [](auto ai, auto bi) { return ai * bi; }); > >> > > >> > > ^ > >> > > >> > > error: ‘ai’ was not declared in this scope > >> > > >> > > [](auto ai, auto bi) { return ai * bi; }); > >> > > >> > > ^ > >> > > >> > > error: ‘bi’ was not declared in this scope > >> > > >> > > [](auto ai, auto bi) { return ai * bi; }); > >> > > >> > > ^ > >> > > >> > can be reproduced with gcc v4.8.5. Many of the other error > >> messages can > >> > > >> > be reproduced by more recent gcc versions with the C++11 flag. The > >> > > >> > minimal gcc version needed for espresso 4.1 is v4.9.0. Our build > >> system > >> > > >> > does not check for compiler version numbers, instead it checks the > >> > > >> > compiler is C++14-capable. I'm not sure why CMake did not fail. Also, > >> > > >> > the CMake output should have shown a line with the compiler > >> version, or > >> > > >> > the string "The CXX compiler identification is unknown". > >> > > >> > Could you please share with us your CMake version and gcc > >> version? The > >> > > >> > command lines are "gcc --version" and "cmake --version". If this > >> is an > >> > > >> > issue in CMake, we will have to add a few lines in our build system. > >> > > >> > Best, > >> > > >> > JN > >> > > >> > On 10/3/19 5:22 PM, Shawn wrote: > >> > > >> >> Hi JN, > >> > > >> >> > >> > > >> >> As you mentioned in your reply, I deleted the old folder of 4.0.2, > >> > > >> >> unpacked the files of 4.1.0 and tried to reinstall the newest > >> package, > >> > > >> >> but the errors still existed during the compilation. Attached > >> please > >> > > >> >> find the output. > >> > > >> >> > >> > > >> >> Mainly two problems: > >> > > >> >> > >> > > >> >> 1 fatal: Not a git repository (or any of the parent > >> directories): .git > >> > > >> >> > >> > > >> >> 2 At global scope: > >> > > >> >> > >> > > >> >> cc1plus: warning: unrecognized command line option > >> > > >> >> "-Wno-cast-function-type" [enabled by default] > >> > > >> >> > >> > > >> >> make[2]: *** [src/core/CMakeFiles/EspressoCore.dir/cells.cpp.o] > >> Error 1 > >> > > >> >> > >> > > >> >> make[1]: *** [src/core/CMakeFiles/EspressoCore.dir/all] Error 2 > >> > > >> >> > >> > > >> >> make: *** [all] Error 2 > >> > > >> >> > >> > > >> >> Could you help me to figure out what’s the reason why I failed ? > >> > > >> >> > >> > > >> >> Thank you very much. > >> > > >> >> > >> > > >> >> Best, > >> > > >> >> > >> > > >> >> Shawn > >> > > >> >> > >> > > >> >> *发件人: *Jean-Noël Grad <mailto:address@hidden > >> <mailto:address@hidden>> > >> > > >> >> *发送时间: *2019年10月2日17:19 > >> > > >> >> *收件人: *address@hidden > >> <mailto:address@hidden> > >> <mailto:address@hidden > >> <mailto:address@hidden>> > >> > > >> >> *主题: *Re: [ESPResSo-users] Problem with installation of > >> espresso-4.1.0 > >> > > >> >> > >> > > >> >> Hi Shawn, > >> > > >> >> > >> > > >> >> The g++ error message is hard to interpret. The include paths > >> are wrong, > >> > > >> >> > >> > > >> >> there is an extra folder > >> /home/zhsh/sourcecode/espresso/src/core/utils > >> > > >> >> > >> > > >> >> that shouldn't exist, and the compiler options do not match what > >> we have > >> > > >> >> > >> > > >> >> in 4.1.0. Could it be that you accidentally unpacked the files > >> of the > >> > > >> >> > >> > > >> >> 4.1.0 release into the same folder where you unpacked the files > >> of the > >> > > >> >> > >> > > >> >> 4.0.2 release back in July? > >> > > >> >> > >> > > >> >> Best, > >> > > >> >> > >> > > >> >> JN > >> > > >> >> > >> > > >> >> On 10/2/19 8:47 PM, Shawn wrote: > >> > > >> >> > >> > > >> >>> Hello guys, > >> > > >> >> > >> > > >> >>> As the newest version of espresso released, I am trying to > >> install it on > >> > > >> >> > >> > > >> >>> my computer. But I got an fatal error when I tried to compile the > >> > > >> >> > >> > > >> >>> package. And I also failed after I ran the "make" command. > >> > > >> >> > >> > > >> >>> Attached please find the detailed output of the compilation. I > >> have used > >> > > >> >> > >> > > >> >>> the same script to install espresso-4.0.2 successfully, but > >> I've no idea > >> > > >> >> > >> > > >> >>> where these errors come from when I try to install > >> espresso-4.1.0. Can > >> > > >> >> > >> > > >> >>> someone help me out? Thank you. > >> > > >> >> > >> > > >> >>> > >> > > >> >> > >> > > >> >>> Best, > >> > > >> >> > >> > > >> >>> Shawn > >> > > >> >> > >> > > >> >>> > >> > > >> >> > >> > > >> > |
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