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 <mailto:address@hidden>
*发送时间: *2019年10月4日5:52
*收件人: *address@hidden <mailto: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,
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
>
>>
>
>>>
>
>>
>