[QE-users] Error during compilation in the step of make all command

Sat Sep 21 16:28:51 CEST 2019

Do you see binaries the /Path/To/QE/Binaries?

Will DeBenedetti
Cornell University

Sent from my iPad

On Sep 21, 2019, at 10:22 AM, 林聖智 <r03223130 at ntu.edu.tw<mailto:r03223130 at ntu.edu.tw>> wrote:

Dear all,

I've successfully complied (at least, I think so) after I updated the version of my mpich to the same as that of my gcc. However, there was the absence of messages, such as that make[2]: leaving directory... and that make[1] ..., in the end of compiling. So, I am wondering whether I install QE successfully.

If not so, how can I fix it?

Best,
Sheng-Chih

從我的 iPhone 傳送
林聖智 <r03223130 at ntu.edu.tw<mailto:r03223130 at ntu.edu.tw>> 於 2019年9月21日 下午2:15 寫道：

Hi Marzari,

Thanks so much for the info. I will try the application later.

Best,
Sheng-Chih Lin
r03223130 at ntu.edu.tw<mailto:r03223130 at ntu.edu.tw>

Marzari Nicola <nicola.marzari at epfl.ch<mailto:nicola.marzari at epfl.ch>> 於 2019年9月21日 下午1:52 寫道：

A very simple solution is to run QE from the Quantum Mobile - https://www.materialscloud.org/work/quantum-mobile .

This is a Ubuntu virtual machine ready to run under MacOs, Windows, Linux, Solaris with Quantum ESPRESSO and all the other MaX codes ready to go (MaX is the European Centre of Excellence for materials science codes).

Nicola

Sent from a tiny keyboard... Contact info:
http://theossrv1.epfl.ch/Main/Contact

On 21 Sep 2019, at 05:46, 林聖智 <r03223130 at ntu.edu.tw<mailto:r03223130 at ntu.edu.tw>> wrote:

Hi Will,

Following the last mail, I’ve checked the status of the QE, after using ./configure. And the checking information showed that QE system detected the Fortran complier and also a parallel environment (I think I used the MPICH environment).

Thank you for considering my request.
Sheng-Chih Lin
r03223130 at ntu.edu.tw<mailto:r03223130 at ntu.edu.tw>

林聖智 <r03223130 at ntu.edu.tw<mailto:r03223130 at ntu.edu.tw>> 於 2019年9月21日 上午11:26 寫道：

Hi Will,

Sorry, I wasn’t clear in the moment, and thanks for reaching out to me. My macOS system is the version of 10.13, and the version of gFortran is that of 8.3.0.

Also, I think I don’t use the parallel environment, although I have installed the Intel Parallel. As for your third concern, I think I haven’t edited the make.in<http://make.in/>c file, since the way I installed the QE was follow the instruction in the file of README. And when I used the ./configure, I did not include specific options. Would it be a problem?

Thank you for considering my request.
Sheng-Chih Lin
r03223130 at ntu.edu.tw<mailto:r03223130 at ntu.edu.tw>

Will DeBenedetti <wjd74 at cornell.edu<mailto:wjd74 at cornell.edu>> 於 2019年9月20日 上午1:06 寫道：

I have QE successfully compiled and linked on macOS 10.14 and 10.13 on 2015 MacBook Pros with i7 processors, albeit using version 6.4.1 and the iFort compilers with MPICH. The make.include file had to be heavily edited to the correct paths to the MKL libs etc. whereas older versions of QE (5.4(ish) and macOS would detect the libraries and parallel environment without issues.

I would try making one binary instead of using 'make all' if you are troubleshooting. Also, if you have later versions of macOS system integrity protection will mess up being able to call QE from just about everything besides the command line (and sometimes even that). You're kind of leaving us in the dark in terms of your setup and how you are approaching the configuration.

What version of gFortran are you using?
Are you using a parallel environment? If so, are you using openMPI or MPICH?
Have you edited the make.inc file correctly?
If you are using ./configure, what are the [options] you are including (if any)?
Can you give some more information re. your system info? i.e. number of processors etc. macOS version?

Will DeBenedetti
Cornell University

On Thu, Sep 19, 2019 at 10:10 AM 林聖智 <r03223130 at ntu.edu.tw<mailto:r03223130 at ntu.edu.tw>> wrote:
Besides, is there a way that I can edit the file of cell_base.f90? I think I could add some options to it and then carry out the calculation of vc_relax using the ‘ibrav’ for the cell_dofree description. But, thus far, I couldn’t find out the Module file when QE was installed using MacPorts.

Thank you for considering my request.
Sheng-Chih Lin
r03223130 at ntu.edu.tw<mailto:r03223130 at ntu.edu.tw>

Paolo Giannozzi <p.giannozzi at gmail.com<mailto:p.giannozzi at gmail.com>> 於 2019年9月19日 下午9:03 寫道：

I see. For some reason the configure of FoX selects a different version of gfortran than the one selected by the configure of QE. Any Macintosh lover out there?

Paolo

On Thu, Sep 19, 2019 at 2:57 PM 林聖智 <r03223130 at ntu.edu.tw<mailto:r03223130 at ntu.edu.tw>> wrote:
Hi Paolo,

Following the last mail, after failing to install the version 6.4, I went back to that of 6.3. Yet, this time I didn’t use MacPorts to install it, but used steps of ./configure and make all to carry the installation. And, the installation did not work. After that, I used MacPorts to install the version 6.3 successfully.

Hope this piece of information can help identify the problem with the manual installation in my computer.

Thank you for considering my request.
Sheng-Chih Lin
r03223130 at ntu.edu.tw<mailto:r03223130 at ntu.edu.tw>

林聖智 <r03223130 at ntu.edu.tw<mailto:r03223130 at ntu.edu.tw>> 於 2019年9月19日 下午8:37 寫道：

Hi Paolo,

Thanks again for your kind help. I originally used MacPorts to install quantum-espresso 6.3, and I thought there might be a conflict between two versions, so I then uninstalled 6.3 first and complied again. However, the message, as follows, just kept showing up. And I also tried the command - make clean, but was no joy, either.

fox_init_module.f90:5:4:

 USE m_common_io, ONLY: setup_io, io_err, io_eor, io_eof
    1
Fatal Error: Cannot read module file 'm_common_io.mod' opened at (1), because it was created by a different version of GNU Fortran

Also, when I make clean, the FoX file would automatically disappear as well, so I am confused with your instruction of removing the directory FoX.

Thank you for considering my request.
Sheng-Chih Lin
r03223130 at ntu.edu.tw<mailto:r03223130 at ntu.edu.tw>

Paolo Giannozzi <p.giannozzi at gmail.com<mailto:p.giannozzi at gmail.com>> 於 2019年9月19日 下午4:33 寫道：

Remove the directory FoX/ and recompile - Paolo

On Thu, Sep 19, 2019 at 8:37 AM 林聖智 <r03223130 at ntu.edu.tw<mailto:r03223130 at ntu.edu.tw>> wrote:
Dear Paolo Giannozzi,

Thanks for the reply. I do use the command of make clean, but still cannot compile completely.

Best,
Sheng-Chih

> Paolo Giannozzi <p.giannozzi at gmail.com<mailto:p.giannozzi at gmail.com>> 於 2019年9月19日 下午2:29 寫道：
>
> Fortran

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Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222

_______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso<http://www.max-centre.eu/quantum-espresso>)
users mailing list users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>
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_______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso<http://www.max-centre.eu/quantum-espresso>)
users mailing list users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>
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_______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso<http://www.max-centre.eu/quantum-espresso>)
users mailing list users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>
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--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222

_______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso<http://www.max-centre.eu/quantum-espresso>)
users mailing list users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>
https://lists.quantum-espresso.org/mailman/listinfo/users

_______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso<http://www.max-centre.eu/quantum-espresso>)
users mailing list users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>
https://lists.quantum-espresso.org/mailman/listinfo/users
_______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso<http://www.max-centre.eu/quantum-espresso>)
users mailing list users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>
https://lists.quantum-espresso.org/mailman/listinfo/users

_______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso<http://www.max-centre.eu/quantum-espresso>)
users mailing list users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>
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_______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso<http://www.max-centre.eu/quantum-espresso>)
users mailing list users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>
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_______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso<http://www.max-centre.eu/quantum-espresso>)
users mailing list users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>
https://lists.quantum-espresso.org/mailman/listinfo/users

_______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso<http://www.max-centre.eu/quantum-espresso>)
users mailing list users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>
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_______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso<http://www.max-centre.eu/quantum-espresso>)
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