[ESPResSo-users] 回复: 回复: 回复: 回复: Problem with installation of espresso

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
发送时间: 2019年10月4日 5:52
收件人: address@hidden
主题: Re: [ESPResSo-users] 回复: 回复: 回复: Problem with installation of espresso-4.1.0

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,

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

>> >

>> >>

>> >

>> >>>

>> >

>> >>

>> >

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