date:20191127

Re: [QE-users] Quantum espresso installation problem in MAC

2019-11-27 Thread Mejia Rodriguez, Daniel

Hi Kanka,

_stdio.h is a header file that comes with Xcode. You should try to update the 
headers with a command similar to

cd /Library/Developer/CommandLineTools/Packages/
open macOS_SDK_headers_for_macOS_10.14.pkg

(This will open an installation wizard). And then compile QE.



Daniel Mejia Rodriguez
Postdoctoral Associate
University of Florida

Get Outlook for Android


From: users  on behalf of Ye Luo 

Sent: Wednesday, November 27, 2019 9:28:32 AM
To: Quantum ESPRESSO users Forum 
Subject: Re: [QE-users] Quantum espresso installation problem in MAC

[External Email]
The error message indicates the gcc8.3 you have installed is not compatible 
with your OS.
QE includes  which is standard C. The stdio.h shipped by the compiler 
tries to access _stdio.h which doesn't exist in the system.
So probably you can write a dummy C program with just include stdio.h and a 
main function and then use it to debug your compiler installation first.
This is not a QE problem and hopefully you can find answers on Google.
Best,k
Ye

===
Ye Luo, Ph.D.
Computational Science Division & Leadership Computing Facility
Argonne National Laboratory


Kanka Ghosh mailto:kanka.gh...@u-bordeaux.fr>> 
于2019年11月26日周二 上午4:45写道：
Hello,

I am trying to install quantum espresso in iMac (macOS Mojave, version 
10.14.6). While it configured properly, I am facing some issues while compiling 
with make all or make pw or any make command. It is showing the following error 
after executing make all command :



make all

test -d bin || mkdir bin

( cd clib ; /Library/Developer/CommandLineTools/usr/bin/make TLDEPS= all || 
exit 1 )

gcc -O3 -D__FFTW3 -D__MPI -I/Users/kghosh/Downloads/qe-6.4.1//include 
-I/Users/kghosh/Downloads/qe-6.4.1//FoX/finclude 
-I/Users/kghosh/Downloads/qe-6.4.1//S3DE/iotk/include/  -c customize_signals.c

gcc -O3 -D__FFTW3 -D__MPI -I/Users/kghosh/Downloads/qe-6.4.1//include 
-I/Users/kghosh/Downloads/qe-6.4.1//FoX/finclude 
-I/Users/kghosh/Downloads/qe-6.4.1//S3DE/iotk/include/  -c stack.c

In file included from stack.c:9:

/usr/local/lib/gcc/x86_64-apple-darwin18.5.0/8.3.0/include-fixed/stdio.h:78:10:fatal
 error: _stdio.h: No such file or directory

 #include <_stdio.h>

  ^~

compilation terminated.

make[1]: *** [stack.o] Error 1

make: *** [libs] Error 1


Can anybody help to overcome this issue ? I have installed all gcc compilers as 
well as the libraries using brew in the machine.

Thanks in advanced,

Kanka
Postdoc, I2M-bordeaux
University of Bordeaux, CNRS UMR 5295
___
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Re: [QE-users] Quantum espresso installation problem in MAC

2019-11-27 Thread Ye Luo

The error message indicates the gcc8.3 you have installed is not compatible
with your OS.
QE includes  which is standard C. The stdio.h shipped by the
compiler tries to access _stdio.h which doesn't exist in the system.
So probably you can write a dummy C program with just include stdio.h and a
main function and then use it to debug your compiler installation first.
This is not a QE problem and hopefully you can find answers on Google.
Best,k
Ye

===
Ye Luo, Ph.D.
Computational Science Division & Leadership Computing Facility
Argonne National Laboratory


Kanka Ghosh  于2019年11月26日周二 上午4:45写道：

> Hello,
>
> I am trying to install quantum espresso in iMac (macOS Mojave, version
> 10.14.6). While it configured properly, I am facing some issues while
> compiling with make all or make pw or any make command. It is showing the
> following error after executing make all command :
>
>
>
> make all
>
> test -d bin || mkdir bin
>
> ( cd clib ; /Library/Developer/CommandLineTools/usr/bin/make TLDEPS= all
> || exit 1 )
>
> gcc -O3 -D__FFTW3 -D__MPI -I/Users/kghosh/Downloads/qe-6.4.1//include
> -I/Users/kghosh/Downloads/qe-6.4.1//FoX/finclude
> -I/Users/kghosh/Downloads/qe-6.4.1//S3DE/iotk/include/  -c
> customize_signals.c
>
> gcc -O3 -D__FFTW3 -D__MPI -I/Users/kghosh/Downloads/qe-6.4.1//include
> -I/Users/kghosh/Downloads/qe-6.4.1//FoX/finclude
> -I/Users/kghosh/Downloads/qe-6.4.1//S3DE/iotk/include/  -c stack.c
>
> In file included from *stack.c:9*:
>
>
> */usr/local/lib/gcc/x86_64-apple-darwin18.5.0/8.3.0/include-fixed/stdio.h:78:10:**fatal
> error: *_stdio.h: No such file or directory
>
>  #include *<_stdio.h>*
>
>   *^~*
>
> compilation terminated.
>
> make[1]: *** [stack.o] Error 1
>
> make: *** [libs] Error 1
>
>
> Can anybody help to overcome this issue ? I have installed all gcc
> compilers as well as the libraries using brew in the machine.
>
> Thanks in advanced,
>
> Kanka
> Postdoc, I2M-bordeaux
> University of Bordeaux, CNRS UMR 5295
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
users mailing list users@lists.quantum-espresso.org
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[QE-users] Improve convergence with noncollinear calculation

2019-11-27 Thread Christoph Wolf

Dear all,

I am having some issues with the energy convergence of a noncollinear
calculation to determine energy difference for different spin alignments.
The expected energies are ~1...5 meV so energy convergence should be rather
tight.

However I find that with high degauss values I cannot reach energy values
with the necessary precision and with low degauss and low conv_thr I never
reach convergence. So I do a restart loop with gradually smaller degauss,
mixing_beta and conv_thr but the resulting "algorithm" is very slow and
despite going to mxiing_beta ~0.01, degauss=0.001 I cannot reach
conv_thr~1D-10

Does anyone have a hint on how to reach the desired conv_thr with
reasonable "speed"? I attach the convergence behavior for decreasing
degauss and mixing_beta (for values where convergence gets tricky: degauss
from 0.005, 0.001, 0.0005, conv_thr=5D-10, beta=10*degauss)

[image: image.png]

electron_maxstep is 60 for all iterations over degauss; I have to mention
that the magnetic momenta do not fluctuate anymore, it seems that there
simply is a lower limit to which convergence I can achieve (?)

Any help is appreciated!

Thanks in advance,
Chris

-- 
Postdoctoral Researcher
Center for Quantum Nanoscience, Institute for Basic Science
Ewha Womans University, Seoul, South Korea
___
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Re: [QE-users] Quantum espresso installation problem in MAC

2019-11-27 Thread Paolo Giannozzi

This is of course _not possible_ if you do things right. Unless you
compiler is broken, of course

On Wed, Nov 27, 2019 at 10:55 AM Kanka Ghosh 
wrote:

> Dear Paolo,
>
> It's still showing the error in compiling !
>
>
> In file included from *stack.c:9*:
>
>
> */usr/local/lib/gcc/x86_64-apple-darwin18.5.0/8.3.0/include-fixed/stdio.h:78:10:**fatal
> error: *_stdio.h: No such file or directory
>
>  #include *<_stdio.h>*
>
>   *^~*
>
> compilation terminated.
>
> make[1]: *** [stack.o] Error 1
>
> make: *** [libs] Error 1
>
> Regards,
> Kanka
> Postdoc, I2M-bordeaux
> University of Bordeaux, CNRS UMR 5295
> --
> *De: *"Paolo Giannozzi" 
> *À: *"users" 
> *Envoyé: *Mardi 26 Novembre 2019 17:37:21
> *Objet: *Re: [QE-users] Quantum espresso installation problem in MAC
>
> Just modify clib/stack.c in such a way that it does nothing, e.g.,
>
> void remove_stack_limit_(void) {;}
>
> It's used only by the Intel compiler actually
>
> Paolo
>
> On Tue, Nov 26, 2019 at 11:45 AM Kanka Ghosh 
> wrote:
>
>> Hello,
>>
>> I am trying to install quantum espresso in iMac (macOS Mojave, version
>> 10.14.6). While it configured properly, I am facing some issues while
>> compiling with make all or make pw or any make command. It is showing the
>> following error after executing make all command :
>>
>>
>>
>> make all
>>
>> test -d bin || mkdir bin
>>
>> ( cd clib ; /Library/Developer/CommandLineTools/usr/bin/make TLDEPS= all
>> || exit 1 )
>>
>> gcc -O3 -D__FFTW3 -D__MPI -I/Users/kghosh/Downloads/qe-6.4.1//include
>> -I/Users/kghosh/Downloads/qe-6.4.1//FoX/finclude
>> -I/Users/kghosh/Downloads/qe-6.4.1//S3DE/iotk/include/  -c
>> customize_signals.c
>>
>> gcc -O3 -D__FFTW3 -D__MPI -I/Users/kghosh/Downloads/qe-6.4.1//include
>> -I/Users/kghosh/Downloads/qe-6.4.1//FoX/finclude
>> -I/Users/kghosh/Downloads/qe-6.4.1//S3DE/iotk/include/  -c stack.c
>>
>> In file included from *stack.c:9*:
>>
>>
>> */usr/local/lib/gcc/x86_64-apple-darwin18.5.0/8.3.0/include-fixed/stdio.h:78:10:**fatal
>> error: *_stdio.h: No such file or directory
>>
>>  #include *<_stdio.h>*
>>
>>   *^~*
>>
>> compilation terminated.
>>
>> make[1]: *** [stack.o] Error 1
>>
>> make: *** [libs] Error 1
>>
>>
>> Can anybody help to overcome this issue ? I have installed all gcc
>> compilers as well as the libraries using brew in the machine.
>>
>> Thanks in advanced,
>>
>> Kanka
>> Postdoc, I2M-bordeaux
>> University of Bordeaux, CNRS UMR 5295
>> ___
>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
>> users mailing list users@lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
>
>
>
> --
> 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)
> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users



-- 
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)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [QE-users] Quantum espresso installation problem in MAC

2019-11-27 Thread Kanka Ghosh

Dear Paolo, 

It's still showing the error in compiling ! 





In file included from stack.c:9 : 

/usr/local/lib/gcc/x86_64-apple-darwin18.5.0/8.3.0/include-fixed/stdio.h:78:10: 
fatal error: _stdio.h: No such file or directory 

#include <_stdio.h> 

^~ 

compilation terminated. 

make[1]: *** [stack.o] Error 1 

make: *** [libs] Error 1 

Regards, 
Kanka 
Postdoc, I2M-bordeaux 
University of Bordeaux, CNRS UMR 5295 

De: "Paolo Giannozzi"  
À: "users"  
Envoyé: Mardi 26 Novembre 2019 17:37:21 
Objet: Re: [QE-users] Quantum espresso installation problem in MAC 

Just modify clib/stack.c in such a way that it does nothing, e.g., 

void remove_stack_limit_(void) {;} 

It's used only by the Intel compiler actually 

Paolo 

On Tue, Nov 26, 2019 at 11:45 AM Kanka Ghosh < [ 
mailto:kanka.gh...@u-bordeaux.fr | kanka.gh...@u-bordeaux.fr ] > wrote: 



Hello, 

I am trying to install quantum espresso in iMac (macOS Mojave, version 
10.14.6). While it configured properly, I am facing some issues while compiling 
with make all or make pw or any make command. It is showing the following error 
after executing make all command : 








make all 

test -d bin || mkdir bin 

( cd clib ; /Library/Developer/CommandLineTools/usr/bin/make TLDEPS= all || 
exit 1 ) 

gcc -O3 -D__FFTW3 -D__MPI -I/Users/kghosh/Downloads/qe-6.4.1//include 
-I/Users/kghosh/Downloads/qe-6.4.1//FoX/finclude 
-I/Users/kghosh/Downloads/qe-6.4.1//S3DE/iotk/include/ -c customize_signals.c 

gcc -O3 -D__FFTW3 -D__MPI -I/Users/kghosh/Downloads/qe-6.4.1//include 
-I/Users/kghosh/Downloads/qe-6.4.1//FoX/finclude 
-I/Users/kghosh/Downloads/qe-6.4.1//S3DE/iotk/include/ -c stack.c 

In file included from stack.c:9 : 

/usr/local/lib/gcc/x86_64-apple-darwin18.5.0/8.3.0/include-fixed/stdio.h:78:10: 
fatal error: _stdio.h: No such file or directory 

#include <_stdio.h> 

^~ 

compilation terminated. 

make[1]: *** [stack.o] Error 1 

make: *** [libs] Error 1 


Can anybody help to overcome this issue ? I have installed all gcc compilers as 
well as the libraries using brew in the machine. 

Thanks in advanced, 

Kanka 
Postdoc, I2M-bordeaux 
University of Bordeaux, CNRS UMR 5295 
___ 
Quantum ESPRESSO is supported by MaX ( [ 
http://www.max-centre.eu/quantum-espresso | www.max-centre.eu/quantum-espresso 
] ) 
users mailing list [ mailto:users@lists.quantum-espresso.org | 
users@lists.quantum-espresso.org ] 
[ https://lists.quantum-espresso.org/mailman/listinfo/users | 
https://lists.quantum-espresso.org/mailman/listinfo/users ] 




-- 
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 


___ 
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users mailing list users@lists.quantum-espresso.org 
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Re: [QE-users] Quantum espresso installation problem in MAC

2019-11-27 Thread Kanka Ghosh

Hi Will, 

This is the MAC.inc file. 
PFA 

Regards, 
Kanka 

De: "Will DeBenedetti"  
À: "users"  
Envoyé: Mardi 26 Novembre 2019 17:31:31 
Objet: Re: [QE-users] Quantum espresso installation problem in MAC 

Hi Kanka, 
I have had the best luck compiling and linking libraries using the Intel 
Fortran compilers and MKL libraries on Macs. I never succeeded with GCC. Can 
you please send your MAKE.inc file? 

Thanks, 

Will DeBenedetti 
Cornell University 

On Tue, Nov 26, 2019 at 5:45 AM Kanka Ghosh < [ 
mailto:kanka.gh...@u-bordeaux.fr | kanka.gh...@u-bordeaux.fr ] > wrote: 



Hello, 

I am trying to install quantum espresso in iMac (macOS Mojave, version 
10.14.6). While it configured properly, I am facing some issues while compiling 
with make all or make pw or any make command. It is showing the following error 
after executing make all command : 








make all 

test -d bin || mkdir bin 

( cd clib ; /Library/Developer/CommandLineTools/usr/bin/make TLDEPS= all || 
exit 1 ) 

gcc -O3 -D__FFTW3 -D__MPI -I/Users/kghosh/Downloads/qe-6.4.1//include 
-I/Users/kghosh/Downloads/qe-6.4.1//FoX/finclude 
-I/Users/kghosh/Downloads/qe-6.4.1//S3DE/iotk/include/ -c customize_signals.c 

gcc -O3 -D__FFTW3 -D__MPI -I/Users/kghosh/Downloads/qe-6.4.1//include 
-I/Users/kghosh/Downloads/qe-6.4.1//FoX/finclude 
-I/Users/kghosh/Downloads/qe-6.4.1//S3DE/iotk/include/ -c stack.c 

In file included from stack.c:9 : 

/usr/local/lib/gcc/x86_64-apple-darwin18.5.0/8.3.0/include-fixed/stdio.h:78:10: 
fatal error: _stdio.h: No such file or directory 

#include <_stdio.h> 

^~ 

compilation terminated. 

make[1]: *** [stack.o] Error 1 

make: *** [libs] Error 1 


Can anybody help to overcome this issue ? I have installed all gcc compilers as 
well as the libraries using brew in the machine. 

Thanks in advanced, 

Kanka 
Postdoc, I2M-bordeaux 
University of Bordeaux, CNRS UMR 5295 
___ 
Quantum ESPRESSO is supported by MaX ( [ 
http://www.max-centre.eu/quantum-espresso | www.max-centre.eu/quantum-espresso 
] ) 
users mailing list [ mailto:users@lists.quantum-espresso.org | 
users@lists.quantum-espresso.org ] 
[ https://lists.quantum-espresso.org/mailman/listinfo/users | 
https://lists.quantum-espresso.org/mailman/listinfo/users ] 



___ 
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make.inc
Description: Binary data
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Re: [QE-users] Quantum espresso installation problem in MAC

Re: [QE-users] Quantum espresso installation problem in MAC

[QE-users] Improve convergence with noncollinear calculation

Re: [QE-users] Quantum espresso installation problem in MAC

Re: [QE-users] Quantum espresso installation problem in MAC

Re: [QE-users] Quantum espresso installation problem in MAC

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