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| From: | Shawn |
| Subject: | [ESPResSo-users] 回复: 回复: 回复: Problem with installation of espresso-4.1.0 |
| Date: | Thu, 3 Oct 2019 17:18:48 -0500 |
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 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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