error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

[jameclear]

ubuntu_16.04.log.txt
there is an error when I execute the python-meep-install.sh.
does this error matters?
need some help.

[FilipDominec]

Hi, thank you for reporting. I can see the first issue comes around the line:

warning "Using deprecated NumPy API... "

I think I have tested the script on ubuntu 16.04 previously and it compiled correctly. Do you have any clue how your system may differ from the default one?

EDIT: I found out that the "deprecated NumPy API" warning is in many previous log files, too, including Ubuntu versions 15.10 and 16.04, where compilation does not fail. So there is some other cause for the python-meep compilation failing.

[jameclear]

Hi, my system is also same with your default one. That's Ubuntu 5.4.0-6ubuntu1~16.04.4 (64bit).

[FilipDominec]

Hi, I would like to exactly reproduce the reported issue, but I could not find Ubuntu 16.04.4 at
https://www.ubuntu.com/download/alternative-downloads

Can you post a link how to get the exact version you use? Thanks!

As a matter of fact, in the logs/ directory I can see that some 16.04.? x64 version was tested a year ago and it worked then, see https://github.com/FilipDominec/python-meep-install/blob/master/logs/160711_ubuntu-16.04-fzu5-withoutMPB.log . So either something changed between the 16.04 minor revisions, or the trouble is in your using MPB, or that some of the changes of this project broke it. Hard to tell unless we try it out.

[jameclear]

Hi，thank you for your kind reply.
Recently, I also have tested the 16.04.3 x64 version using the repository ubuntu-16.04.3-desktop-amd64.iso at http://releases.ubuntu.com/16.04.3/ .
Both of them imply the error :command ‘x86_64-linux-gnu-gcc’ failed with exit status 1.
Then I try to use the meep simulation and it worked well. So something error may occur at the installing the python-meep module.

[FilipDominec]

Interesting indeed...

[FilipDominec]

Dear xdcqu, I spent several hours with an extensive test of the python-meep compilation with different Ubuntu versions, namely

• 16.04 x86_64 (logfile: logs/171009-Ubuntu16.04-x86_64.log)
• 16.04.3 x86_64 (logfile: logs/171009-Ubuntu16.04.3-x86_64.log)
• 16.10 x86_64 (a production machine which also compiled without errors earlier)
• 17.04 x86_64 (logfile: logs/171009-ubuntu-17.04-amd64-GuileFromRepo2.log)
• 17.10 x86_64 (logfile to be added)

The result is that this time I could not replicate the error you reported - that is, SWIG failing during compilation of python-meep starting with the lines of

meep_mpi_wrap.cpp: In function ‘double* new_doubleP()’:
meep_mpi_wrap.cpp:3851:18: error: redefinition of ‘double* new_doubleP()’
...

The "redefinition" messages are perhaps the characteristic of the problem in your attached file ubuntu_16.04.log.txt in your post. As a matter of fact, the same fatal error is found in one log file, namely 171006-ubuntu17.04-amd64-02withguile11fromgit.log where I chose a manual compilation of Guile and this compilation step failed. Weird enough, Guile seems to be installed correctly on your system...

To conclude, everything worked flawlessly in the mentioned Ubuntu versions (except for few unrelated runtime errors). Can you, please, git pull and repeat whole installation, perhaps in freshly installed virtual machine? I believe it will be fine!