[Pw_forum] Quantum Espresso installed, but examples not running

[Alexander Eftimiades]

I hope I came to the right place to ask this question. I have compiled
quantum espresso using this set of instructions:
http://how-to.wikia.com/wiki/How_to_install_PWscf_on_a_Debian_or_Debian_based_operating_system

I made two modifications to these instructions:
I installed version 4.2.1 and put the folder together using these
instructions:http://qe-forge.org/frs/shownotes.php?release_id=64.
These instructions did not say anything about "PLUMED" plugin so I did
not download it.
I have gfortran installed so I did not do the first part of the
instructions (although I later tried to install g95 using the link
provided and it kept saying "authentication failed")

I have openmpi installed but I only have one cpu at the moment (I
intend to set up a network later.)

Everything seemed to work ok so I tried to run one of the examples. I
got this:


/opt/espresso-4.2.1/examples/example08 : starting

This example shows how to use pw.x to calculate the DOS of Ni.

executables directory: /opt/espresso-4.2.1/bin
pseudo directory: /opt/espresso-4.2.1/pseudo
temporary directory: /tmp
checking that needed directories and files exist... done

running pw.x as: /opt/espresso-4.2.1/bin/pw.x
running dos.x as: /opt/espresso-4.2.1/bin/dos.x
running projwfc.x as: /opt/espresso-4.2.1/bin/projwfc.x
running kvecs_FS.x as: /opt/espresso-4.2.1/bin/kvecs_FS.x
running bands_FS.x as: /opt/espresso-4.2.1/bin/bands_FS.x

cleaning /tmp... done
running the scf calculation for Ni...[debian:13270] *** Process
received signal ***
[debian:13270] Signal: Segmentation fault (11)
[debian:13270] Signal code: (128)
[debian:13270] Failing at address: (nil)
[debian:13270] [ 0] [0xb779040c]
[debian:13270] [ 1] /usr/lib/libfftw3.so.3 [0xb6f30d5c]
[debian:13270] [ 2] /usr/lib/libfftw3.so.3 [0xb6f30eca]
[debian:13270] [ 3] /usr/lib/libfftw3.so.3 [0xb6f2e684]
[debian:13270] [ 4] /usr/lib/libfftw3.so.3 [0xb6f33618]
[debian:13270] [ 5] /usr/lib/libfftw3.so.3(dfftw_execute_dft_+0x5c)
[0xb6fa6b7c]
[debian:13270] [ 6] /opt/espresso-4.2.1/bin/
pw.x(__fft_scalar_MOD_cft_1z+0x912) [0x81d0b62]
[debian:13270] [ 7] /opt/espresso-4.2.1/bin/
pw.x(__fft_parallel_MOD_tg_cft3s+0x7d3) [0x81ce9d3]
[debian:13270] [ 8] /opt/espresso-4.2.1/bin/pw.x(cft3_+0x52) [0x807ccd2]
[debian:13270] [ 9] /opt/espresso-4.2.1/bin/pw.x(interpolate_+0x408)
[0x8176848]
[debian:13270] [10] /opt/espresso-4.2.1/bin/pw.x(set_vrs_+0x145)
[0x80f3c25]
[debian:13270] [11] /opt/espresso-4.2.1/bin/pw.x(potinit_+0xc1d)
[0x80cf10d]
[debian:13270] [12] /opt/espresso-4.2.1/bin/pw.x(init_run_+0x44d)
[0x809ceed]
[debian:13270] [13] /opt/espresso-4.2.1/bin/pw.x(MAIN__+0xa2)
[0x8074b82]
[debian:13270] [14] /opt/espresso-4.2.1/bin/pw.x(main+0x39) [0x834acc9]
[debian:13270] [15] /lib/i686/cmov/libc.so.6(__libc_start_main+0xe5)
[0xb67d9455]
[debian:13270] [16] /opt/espresso-4.2.1/bin/pw.x [0x8074a41]
[debian:13270] *** End of error message ***
./run_example: line 174: 13270 Segmentation fault $PW_COMMAND <
ni.scf.in > ni.scf.out
Error condition encountered during test: exit status = 139
Aborting

---------rest of email continues here----------

Similar messages come up for other examples. Could someone please tell
me what is going on? And--yes I read the user manual instructions (and
yes chapter 2). If there is a pointer in there I missed please tell me.
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[Eyvaz Isaev]

Hi,

Usually "Segmentation fault" tells about insufficient memory problem, but it
might be due to a compiler/lib error. I can start pw.x on my Ubuntu 10.04 (in
fact, Debian-based, and quite buggy) with gfortran.

Bests,
Eyvaz.

-------------------------------------------------------------------
Prof. Eyvaz Isaev,
Department of Physics, Chemistry, and Biology (IFM), Linkoping University,
Sweden

Theoretical Physics Department, Moscow State Institute of Steel & Alloys,
Russia,

isaev at ifm.liu.se, eyvaz_isaev at yahoo.com




________________________________
From: Alexander Eftimiades <alexeftimiades at gmail.com>
To: pw_forum at pwscf.org
Sent: Sat, September 11, 2010 8:15:31 PM
Subject: [Pw_forum] Quantum Espresso installed, but examples not running

I hope I came to the right place to ask this question. I have compiled quantum
espresso using this set of instructions:
http://how-to.wikia.com/wiki/How_to_install_PWscf_on_a_Debian_or_Debian_based_operating_system


I made two modifications to these instructions:
1. I installed version 4.2.1 and put the folder together using these
instructions:http://qe-forge.org/frs/shownotes.php?release_id=64. These
instructions did not say anything about "PLUMED" plugin so I did not download
it.
2. I have gfortran installed so I did not do the first part of the instructions
(although I later tried to install g95 using the link provided and it kept
saying "authentication failed")

I have openmpi installed but I only have one cpu at the moment (I intend to set
up a network later.)

Everything seemed to work ok so I tried to run one of the examples. I got this:


/opt/espresso-4.2.1/examples/example08 : starting

This example shows how to use pw.x to calculate the DOS of Ni.

executables directory: /opt/espresso-4.2.1/bin
pseudo directory: /opt/espresso-4.2.1/pseudo
temporary directory: /tmp
checking that needed directories and files exist... done

running pw.x as: /opt/espresso-4.2.1/bin/pw.x
running dos.x as: /opt/espresso-4.2.1/bin/dos.x
running projwfc.x as: /opt/espresso-4.2.1/bin/projwfc.x
running kvecs_FS.x as: /opt/espresso-4.2.1/bin/kvecs_FS.x
running bands_FS.x as: /opt/espresso-4.2.1/bin/bands_FS.x

cleaning /tmp... done
running the scf calculation for Ni...[debian:13270] *** Process received
signal ***
[debian:13270] Signal: Segmentation fault (11)
[debian:13270] Signal code: (128)
[debian:13270] Failing at address: (nil)
[debian:13270] [ 0] [0xb779040c]
[debian:13270] [ 1] /usr/lib/libfftw3.so.3 [0xb6f30d5c]
[debian:13270] [ 2] /usr/lib/libfftw3.so.3 [0xb6f30eca]
[debian:13270] [ 3] /usr/lib/libfftw3.so.3 [0xb6f2e684]
[debian:13270] [ 4] /usr/lib/libfftw3.so.3 [0xb6f33618]
[debian:13270] [ 5] /usr/lib/libfftw3.so.3(dfftw_execute_dft_+0x5c) [0xb6fa6b7c]
[debian:13270] [ 6] /opt/espresso-4.2.1/bin/pw.x(__fft_scalar_MOD_cft_1z+0x912)
[0x81d0b62]
[debian:13270] [ 7]
/opt/espresso-4.2.1/bin/pw.x(__fft_parallel_MOD_tg_cft3s+0x7d3) [0x81ce9d3]
[debian:13270] [ 8] /opt/espresso-4.2.1/bin/pw.x(cft3_+0x52) [0x807ccd2]
[debian:13270] [ 9] /opt/espresso-4.2.1/bin/pw.x(interpolate_+0x408) [0x8176848]
[debian:13270] [10] /opt/espresso-4.2.1/bin/pw.x(set_vrs_+0x145) [0x80f3c25]
[debian:13270] [11] /opt/espresso-4.2.1/bin/pw.x(potinit_+0xc1d) [0x80cf10d]
[debian:13270] [12] /opt/espresso-4.2.1/bin/pw.x(init_run_+0x44d) [0x809ceed]
[debian:13270] [13] /opt/espresso-4.2.1/bin/pw.x(MAIN__+0xa2) [0x8074b82]
[debian:13270] [14] /opt/espresso-4.2.1/bin/pw.x(main+0x39) [0x834acc9]
[debian:13270] [15] /lib/i686/cmov/libc.so.6(__libc_start_main+0xe5)
[0xb67d9455]
[debian:13270] [16] /opt/espresso-4.2.1/bin/pw.x [0x8074a41]
[debian:13270] *** End of error message ***
./run_example: line 174: 13270 Segmentation fault $PW_COMMAND < ni.scf.in >
ni.scf.out
Error condition encountered during test: exit status = 139
Aborting


---------rest of email continues here----------

Similar messages come up for other examples. Could someone please tell me what
is going on? And--yes I read the user manual instructions (and yes chapter 2).
If there is a pointer in there I missed please tell me.



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[Paolo Giannozzi]

Post by Alexander Eftimiades
I hope I came to the right place to ask this question.

you did

Post by Alexander Eftimiades
If there is a pointer in there I missed please tell me.

2.7.1
[...] If you get mysterious errors in the provided tests and
examples: your compiler, or your mathematical
libraries, or MPI libraries, or a combination thereof, is very likely
buggy. Although the presence of subtle
bugs in QUANTUM ESPRESSO that are not revealed during the testing
phase can never be ruled out,
it is very unlikely that this happens on the provided tests and
examples.

10.1.0.9 pw.x crashes with segmentation fault or similarly obscure
messages
Possible reasons:

* too much RAM memory or stack requested (see next item).
* if you are using highly optimized mathematical libraries,
verify that they are designed for your hardware.
* If you are using aggressive optimization in compilation,
verify that you are using the appropriate options for your machine
* The executable was not properly compiled, or was compiled on a
different and incompatible environment.
* buggy compiler or libraries: this is the default explanation
if you have problems with the provided tests and examples.

P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone [phone], fax [phone]

[Alexander Eftimiades]

I should then mention that everything used to compile and execute
Quantum Espresso was built for Debian because it was installed using
synaptic package manager. The large library of packages Synaptic
provides is exactly the reason I use Debian.
I just updated all my software recently so I am quite sure I am using
the latest version of MPI, gfortran, etc Synaptic has to offer.

If you still think my compilers are the problem--any ideas on how I
could go about fixing this. I scoured the web for free ab initio
quantum chemistry software that can calculate phonon dispersion
relations and this definitely seemed to be one of the best. I would
really like to get this running--especially since my projects are not
very different than some of the examples provided.

Post by Paolo Giannozzi

Post by Alexander Eftimiades
I hope I came to the right place to ask this question.

you did

Post by Alexander Eftimiades
If there is a pointer in there I missed please tell me.

2.7.1
[...] If you get mysterious errors in the provided tests and
examples: your compiler, or your mathematical
libraries, or MPI libraries, or a combination thereof, is very likely
buggy. Although the presence of subtle
bugs in QUANTUM ESPRESSO that are not revealed during the testing
phase can never be ruled out,
it is very unlikely that this happens on the provided tests and
examples.
10.1.0.9 pw.x crashes with segmentation fault or similarly obscure
messages
* too much RAM memory or stack requested (see next item).
* if you are using highly optimized mathematical libraries,
verify that they are designed for your hardware.
* If you are using aggressive optimization in compilation,
verify that you are using the appropriate options for your machine
* The executable was not properly compiled, or was compiled on a
different and incompatible environment.
* buggy compiler or libraries: this is the default explanation
if you have problems with the provided tests and examples.
P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone [phone], fax [phone]
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum

[Alexander Eftimiades]

I should then mention that everything used to compile and execute
Quantum Espresso was built for Debian because it was installed using
synaptic package manager. The large library of packages Synaptic
provides is exactly the reason I use Debian.
I just updated all my software recently so I am quite sure I am using
the latest version of MPI, gfortran, etc Synaptic has to offer.

If you still think my compilers are the problem--any ideas on how I
could go about fixing this. I scoured the web for free ab initio
quantum chemistry software that can calculate phonon dispersion
relations and this definitely seemed to be one of the best. I would
really like to get this running--especially since my projects are not
very different than some of the examples provided.

Post by Paolo Giannozzi

Post by Alexander Eftimiades
I hope I came to the right place to ask this question.

you did

Post by Alexander Eftimiades
If there is a pointer in there I missed please tell me.

2.7.1
[...] If you get mysterious errors in the provided tests and
examples: your compiler, or your mathematical
libraries, or MPI libraries, or a combination thereof, is very likely
buggy. Although the presence of subtle
bugs in QUANTUM ESPRESSO that are not revealed during the testing
phase can never be ruled out,
it is very unlikely that this happens on the provided tests and
examples.
10.1.0.9 pw.x crashes with segmentation fault or similarly obscure
messages
* too much RAM memory or stack requested (see next item).
* if you are using highly optimized mathematical libraries,
verify that they are designed for your hardware.
* If you are using aggressive optimization in compilation,
verify that you are using the appropriate options for your machine
* The executable was not properly compiled, or was compiled on a
different and incompatible environment.
* buggy compiler or libraries: this is the default explanation
if you have problems with the provided tests and examples.
P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone [phone], fax [phone]
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum

[Paolo Giannozzi]

Post by Alexander Eftimiades
[debian:13270] [ 1] /usr/lib/libfftw3.so.3 [0xb6f30d5c]

if this message appears for all errors, compile internal
FFTW instead of using external FFTW v.3: in make.sys
replace -D__FFTW3 with -D__FFTW and remove -lfftw3
from libraries, delete all objects that depend upon such
options (rm Modules/fft_scalar.o clib/fft_stick.o should
be enough), recompile

P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone [phone], fax [phone]

[Alexander Eftimiades]

I am not sure what you mean by "internal." I installed libfftw3 and
dev-libfftw3 from Synaptic Package manager.

I am sorry, but I am still relatively new to linux, what should I do
to compile "internal" FFTW?

Post by Paolo Giannozzi

Post by Alexander Eftimiades
[debian:13270] [ 1] /usr/lib/libfftw3.so.3 [0xb6f30d5c]

if this message appears for all errors, compile internal
FFTW instead of using external FFTW v.3: in make.sys
replace -D__FFTW3 with -D__FFTW and remove -lfftw3
from libraries, delete all objects that depend upon such
options (rm Modules/fft_scalar.o clib/fft_stick.o should
be enough), recompile
P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone [phone], fax [phone]
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum

[mohsen modaresi]

Perhaps it is not the best way, but i think if you uninstall FFTW from
Synaptic esperesso use internal FFTW.


On Sun, Sep 12, 2010 at 1:15 AM, Alexander Eftimiades <

Post by Alexander Eftimiades
I am not sure what you mean by "internal." I installed libfftw3 and
dev-libfftw3 from Synaptic Package manager.
I am sorry, but I am still relatively new to linux, what should I do
to compile "internal" FFTW?

Post by Paolo Giannozzi

Post by Alexander Eftimiades
[debian:13270] [ 1] /usr/lib/libfftw3.so.3 [0xb6f30d5c]

if this message appears for all errors, compile internal
FFTW instead of using external FFTW v.3: in make.sys
replace -D__FFTW3 with -D__FFTW and remove -lfftw3
from libraries, delete all objects that depend upon such
options (rm Modules/fft_scalar.o clib/fft_stick.o should
be enough), recompile
P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone [phone], fax [phone]
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum

_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum

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[Alexander Eftimiades]

If I uninstall FFTW from synaptic then synaptic will uninstall quite a
few other packages. What about:
Paolo Giannozzi's suggestion--
If this message appears for all errors, compile internal
FFTW instead of using external FFTW v.3: in make.sys
replace -D__FFTW3 with -D__FFTW and remove -lfftw3
from libraries, delete all objects that depend upon such
options (rm Modules/fft_scalar.o clib/fft_stick.o should
be enough), recompile

I still do not know what you mean by "internal"? Do you mean Quantum
Espresso comes with FFTW? Do I have to download/install anything or do
I just set these variables in the make.sys file and compile as usual?

Post by mohsen modaresi
Perhaps it is not the best way, but i think if you uninstall FFTW
from Synaptic esperesso use internal FFTW.
On Sun, Sep 12, 2010 at 1:15 AM, Alexander Eftimiades <alexeftimiades at gmail.com
I am not sure what you mean by "internal." I installed libfftw3 and
dev-libfftw3 from Synaptic Package manager.
I am sorry, but I am still relatively new to linux, what should I do
to compile "internal" FFTW?

Post by Paolo Giannozzi

Post by Alexander Eftimiades
[debian:13270] [ 1] /usr/lib/libfftw3.so.3 [0xb6f30d5c]

if this message appears for all errors, compile internal
FFTW instead of using external FFTW v.3: in make.sys
replace -D__FFTW3 with -D__FFTW and remove -lfftw3
from libraries, delete all objects that depend upon such
options (rm Modules/fft_scalar.o clib/fft_stick.o should
be enough), recompile
P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone [phone], fax [phone]
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum

_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum

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[Alexander Eftimiades]

If I uninstall FFTW from synaptic then synaptic will uninstall quite a
few other packages. What about:
Paolo Giannozzi's suggestion--
If this message appears for all errors, compile internal
FFTW instead of using external FFTW v.3: in make.sys
replace -D__FFTW3 with -D__FFTW and remove -lfftw3
from libraries, delete all objects that depend upon such
options (rm Modules/fft_scalar.o clib/fft_stick.o should
be enough), recompile

I still do not know what you mean by "internal"? Do you mean Quantum
Espresso comes with FFTW? Do I have to download/install anything or do
I just set these variables in the make.sys file and compile as usual?

Post by mohsen modaresi
Perhaps it is not the best way, but i think if you uninstall FFTW
from Synaptic esperesso use internal FFTW.
On Sun, Sep 12, 2010 at 1:15 AM, Alexander Eftimiades <alexeftimiades at gmail.com
I am not sure what you mean by "internal." I installed libfftw3 and
dev-libfftw3 from Synaptic Package manager.
I am sorry, but I am still relatively new to linux, what should I do
to compile "internal" FFTW?

Post by Paolo Giannozzi

Post by Alexander Eftimiades
[debian:13270] [ 1] /usr/lib/libfftw3.so.3 [0xb6f30d5c]

if this message appears for all errors, compile internal
FFTW instead of using external FFTW v.3: in make.sys
replace -D__FFTW3 with -D__FFTW and remove -lfftw3
from libraries, delete all objects that depend upon such
options (rm Modules/fft_scalar.o clib/fft_stick.o should
be enough), recompile
P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone [phone], fax [phone]
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum

_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum

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[Paolo Giannozzi]

Post by Alexander Eftimiades
I am sorry, but I am still relatively new to linux, what should I do
to compile "internal" FFTW?

in make.sys replace -D__FFTW3 with -D__FFTW and
remove -lfftw3 from libraries, delete all objects that
depend upon such options ("rm Modules/fft_scalar.o clib/fft_stick.o"

maybe you also need a "rm clib/clib.a", just in case

Post by Alexander Eftimiades

should be enough), recompile

"make pwall" or "make all" depending on what you need.

P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone [phone], fax [phone]

[Alexander Eftimiades]

Thank you, that seemed to work well.

Post by Paolo Giannozzi

Post by Alexander Eftimiades
I am sorry, but I am still relatively new to linux, what should I do
to compile "internal" FFTW?

in make.sys replace -D__FFTW3 with -D__FFTW and
remove -lfftw3 from libraries, delete all objects that
depend upon such options ("rm Modules/fft_scalar.o clib/fft_stick.o"

maybe you also need a "rm clib/clib.a", just in case

Post by Alexander Eftimiades

should be enough), recompile

"make pwall" or "make all" depending on what you need.
P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone [phone], fax [phone]
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum

[Alexander Eftimiades]

Thank you, that seemed to work well.

Post by Paolo Giannozzi

Post by Alexander Eftimiades
I am sorry, but I am still relatively new to linux, what should I do
to compile "internal" FFTW?

in make.sys replace -D__FFTW3 with -D__FFTW and
remove -lfftw3 from libraries, delete all objects that
depend upon such options ("rm Modules/fft_scalar.o clib/fft_stick.o"

maybe you also need a "rm clib/clib.a", just in case

Post by Alexander Eftimiades

should be enough), recompile

"make pwall" or "make all" depending on what you need.
P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone [phone], fax [phone]
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum

[mohsen modaresi]

Perhaps it is not the best way, but i think if you uninstall FFTW from
Synaptic esperesso use internal FFTW.


On Sun, Sep 12, 2010 at 1:15 AM, Alexander Eftimiades <

Post by Alexander Eftimiades
I am not sure what you mean by "internal." I installed libfftw3 and
dev-libfftw3 from Synaptic Package manager.
I am sorry, but I am still relatively new to linux, what should I do
to compile "internal" FFTW?

Post by Paolo Giannozzi

Post by Alexander Eftimiades
[debian:13270] [ 1] /usr/lib/libfftw3.so.3 [0xb6f30d5c]

if this message appears for all errors, compile internal
FFTW instead of using external FFTW v.3: in make.sys
replace -D__FFTW3 with -D__FFTW and remove -lfftw3
from libraries, delete all objects that depend upon such
options (rm Modules/fft_scalar.o clib/fft_stick.o should
be enough), recompile
P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone [phone], fax [phone]
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum

_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum

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[Paolo Giannozzi]

Post by Alexander Eftimiades
I am sorry, but I am still relatively new to linux, what should I do
to compile "internal" FFTW?

in make.sys replace -D__FFTW3 with -D__FFTW and
remove -lfftw3 from libraries, delete all objects that
depend upon such options ("rm Modules/fft_scalar.o clib/fft_stick.o"

maybe you also need a "rm clib/clib.a", just in case

Post by Alexander Eftimiades

should be enough), recompile

"make pwall" or "make all" depending on what you need.

P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone [phone], fax [phone]

[Alexander Eftimiades]

I am not sure what you mean by "internal." I installed libfftw3 and
dev-libfftw3 from Synaptic Package manager.

I am sorry, but I am still relatively new to linux, what should I do
to compile "internal" FFTW?

Post by Paolo Giannozzi

Post by Alexander Eftimiades
[debian:13270] [ 1] /usr/lib/libfftw3.so.3 [0xb6f30d5c]

if this message appears for all errors, compile internal
FFTW instead of using external FFTW v.3: in make.sys
replace -D__FFTW3 with -D__FFTW and remove -lfftw3
from libraries, delete all objects that depend upon such
options (rm Modules/fft_scalar.o clib/fft_stick.o should
be enough), recompile
P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone [phone], fax [phone]
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum

[Alexander Eftimiades]

I hope I came to the right place to ask this question. I have compiled
quantum espresso using this set of instructions:
http://how-to.wikia.com/wiki/How_to_install_PWscf_on_a_Debian_or_Debian_based_operating_system

I made two modifications to these instructions:
I installed version 4.2.1 and put the folder together using these
instructions:http://qe-forge.org/frs/shownotes.php?release_id=64.
These instructions did not say anything about "PLUMED" plugin so I did
not download it.
I have gfortran installed so I did not do the first part of the
instructions (although I later tried to install g95 using the link
provided and it kept saying "authentication failed")

I have openmpi installed but I only have one cpu at the moment (I
intend to set up a network later.)

Everything seemed to work ok so I tried to run one of the examples. I
got this:


/opt/espresso-4.2.1/examples/example08 : starting

This example shows how to use pw.x to calculate the DOS of Ni.

executables directory: /opt/espresso-4.2.1/bin
pseudo directory: /opt/espresso-4.2.1/pseudo
temporary directory: /tmp
checking that needed directories and files exist... done

running pw.x as: /opt/espresso-4.2.1/bin/pw.x
running dos.x as: /opt/espresso-4.2.1/bin/dos.x
running projwfc.x as: /opt/espresso-4.2.1/bin/projwfc.x
running kvecs_FS.x as: /opt/espresso-4.2.1/bin/kvecs_FS.x
running bands_FS.x as: /opt/espresso-4.2.1/bin/bands_FS.x

cleaning /tmp... done
running the scf calculation for Ni...[debian:13270] *** Process
received signal ***
[debian:13270] Signal: Segmentation fault (11)
[debian:13270] Signal code: (128)
[debian:13270] Failing at address: (nil)
[debian:13270] [ 0] [0xb779040c]
[debian:13270] [ 1] /usr/lib/libfftw3.so.3 [0xb6f30d5c]
[debian:13270] [ 2] /usr/lib/libfftw3.so.3 [0xb6f30eca]
[debian:13270] [ 3] /usr/lib/libfftw3.so.3 [0xb6f2e684]
[debian:13270] [ 4] /usr/lib/libfftw3.so.3 [0xb6f33618]
[debian:13270] [ 5] /usr/lib/libfftw3.so.3(dfftw_execute_dft_+0x5c)
[0xb6fa6b7c]
[debian:13270] [ 6] /opt/espresso-4.2.1/bin/
pw.x(__fft_scalar_MOD_cft_1z+0x912) [0x81d0b62]
[debian:13270] [ 7] /opt/espresso-4.2.1/bin/
pw.x(__fft_parallel_MOD_tg_cft3s+0x7d3) [0x81ce9d3]
[debian:13270] [ 8] /opt/espresso-4.2.1/bin/pw.x(cft3_+0x52) [0x807ccd2]
[debian:13270] [ 9] /opt/espresso-4.2.1/bin/pw.x(interpolate_+0x408)
[0x8176848]
[debian:13270] [10] /opt/espresso-4.2.1/bin/pw.x(set_vrs_+0x145)
[0x80f3c25]
[debian:13270] [11] /opt/espresso-4.2.1/bin/pw.x(potinit_+0xc1d)
[0x80cf10d]
[debian:13270] [12] /opt/espresso-4.2.1/bin/pw.x(init_run_+0x44d)
[0x809ceed]
[debian:13270] [13] /opt/espresso-4.2.1/bin/pw.x(MAIN__+0xa2)
[0x8074b82]
[debian:13270] [14] /opt/espresso-4.2.1/bin/pw.x(main+0x39) [0x834acc9]
[debian:13270] [15] /lib/i686/cmov/libc.so.6(__libc_start_main+0xe5)
[0xb67d9455]
[debian:13270] [16] /opt/espresso-4.2.1/bin/pw.x [0x8074a41]
[debian:13270] *** End of error message ***
./run_example: line 174: 13270 Segmentation fault $PW_COMMAND <
ni.scf.in > ni.scf.out
Error condition encountered during test: exit status = 139
Aborting

---------rest of email continues here----------

Similar messages come up for other examples. Could someone please tell
me what is going on? And--yes I read the user manual instructions (and
yes chapter 2). If there is a pointer in there I missed please tell me.
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[Eyvaz Isaev]

Hi,

Usually "Segmentation fault" tells about insufficient memory problem, but it
might be due to a compiler/lib error. I can start pw.x on my Ubuntu 10.04 (in
fact, Debian-based, and quite buggy) with gfortran.

Bests,
Eyvaz.

-------------------------------------------------------------------
Prof. Eyvaz Isaev,
Department of Physics, Chemistry, and Biology (IFM), Linkoping University,
Sweden

Theoretical Physics Department, Moscow State Institute of Steel & Alloys,
Russia,

isaev at ifm.liu.se, eyvaz_isaev at yahoo.com




________________________________
From: Alexander Eftimiades <alexeftimiades at gmail.com>
To: pw_forum at pwscf.org
Sent: Sat, September 11, 2010 8:15:31 PM
Subject: [Pw_forum] Quantum Espresso installed, but examples not running

I hope I came to the right place to ask this question. I have compiled quantum
espresso using this set of instructions:
http://how-to.wikia.com/wiki/How_to_install_PWscf_on_a_Debian_or_Debian_based_operating_system


I made two modifications to these instructions:
1. I installed version 4.2.1 and put the folder together using these
instructions:http://qe-forge.org/frs/shownotes.php?release_id=64. These
instructions did not say anything about "PLUMED" plugin so I did not download
it.
2. I have gfortran installed so I did not do the first part of the instructions
(although I later tried to install g95 using the link provided and it kept
saying "authentication failed")

I have openmpi installed but I only have one cpu at the moment (I intend to set
up a network later.)

Everything seemed to work ok so I tried to run one of the examples. I got this:


/opt/espresso-4.2.1/examples/example08 : starting

This example shows how to use pw.x to calculate the DOS of Ni.

executables directory: /opt/espresso-4.2.1/bin
pseudo directory: /opt/espresso-4.2.1/pseudo
temporary directory: /tmp
checking that needed directories and files exist... done

running pw.x as: /opt/espresso-4.2.1/bin/pw.x
running dos.x as: /opt/espresso-4.2.1/bin/dos.x
running projwfc.x as: /opt/espresso-4.2.1/bin/projwfc.x
running kvecs_FS.x as: /opt/espresso-4.2.1/bin/kvecs_FS.x
running bands_FS.x as: /opt/espresso-4.2.1/bin/bands_FS.x

cleaning /tmp... done
running the scf calculation for Ni...[debian:13270] *** Process received
signal ***
[debian:13270] Signal: Segmentation fault (11)
[debian:13270] Signal code: (128)
[debian:13270] Failing at address: (nil)
[debian:13270] [ 0] [0xb779040c]
[debian:13270] [ 1] /usr/lib/libfftw3.so.3 [0xb6f30d5c]
[debian:13270] [ 2] /usr/lib/libfftw3.so.3 [0xb6f30eca]
[debian:13270] [ 3] /usr/lib/libfftw3.so.3 [0xb6f2e684]
[debian:13270] [ 4] /usr/lib/libfftw3.so.3 [0xb6f33618]
[debian:13270] [ 5] /usr/lib/libfftw3.so.3(dfftw_execute_dft_+0x5c) [0xb6fa6b7c]
[debian:13270] [ 6] /opt/espresso-4.2.1/bin/pw.x(__fft_scalar_MOD_cft_1z+0x912)
[0x81d0b62]
[debian:13270] [ 7]
/opt/espresso-4.2.1/bin/pw.x(__fft_parallel_MOD_tg_cft3s+0x7d3) [0x81ce9d3]
[debian:13270] [ 8] /opt/espresso-4.2.1/bin/pw.x(cft3_+0x52) [0x807ccd2]
[debian:13270] [ 9] /opt/espresso-4.2.1/bin/pw.x(interpolate_+0x408) [0x8176848]
[debian:13270] [10] /opt/espresso-4.2.1/bin/pw.x(set_vrs_+0x145) [0x80f3c25]
[debian:13270] [11] /opt/espresso-4.2.1/bin/pw.x(potinit_+0xc1d) [0x80cf10d]
[debian:13270] [12] /opt/espresso-4.2.1/bin/pw.x(init_run_+0x44d) [0x809ceed]
[debian:13270] [13] /opt/espresso-4.2.1/bin/pw.x(MAIN__+0xa2) [0x8074b82]
[debian:13270] [14] /opt/espresso-4.2.1/bin/pw.x(main+0x39) [0x834acc9]
[debian:13270] [15] /lib/i686/cmov/libc.so.6(__libc_start_main+0xe5)
[0xb67d9455]
[debian:13270] [16] /opt/espresso-4.2.1/bin/pw.x [0x8074a41]
[debian:13270] *** End of error message ***
./run_example: line 174: 13270 Segmentation fault $PW_COMMAND < ni.scf.in >
ni.scf.out
Error condition encountered during test: exit status = 139
Aborting


---------rest of email continues here----------

Similar messages come up for other examples. Could someone please tell me what
is going on? And--yes I read the user manual instructions (and yes chapter 2).
If there is a pointer in there I missed please tell me.



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[Paolo Giannozzi]

Post by Alexander Eftimiades
I hope I came to the right place to ask this question.

you did

Post by Alexander Eftimiades
If there is a pointer in there I missed please tell me.

2.7.1
[...] If you get mysterious errors in the provided tests and
examples: your compiler, or your mathematical
libraries, or MPI libraries, or a combination thereof, is very likely
buggy. Although the presence of subtle
bugs in QUANTUM ESPRESSO that are not revealed during the testing
phase can never be ruled out,
it is very unlikely that this happens on the provided tests and
examples.

10.1.0.9 pw.x crashes with segmentation fault or similarly obscure
messages
Possible reasons:

* too much RAM memory or stack requested (see next item).
* if you are using highly optimized mathematical libraries,
verify that they are designed for your hardware.
* If you are using aggressive optimization in compilation,
verify that you are using the appropriate options for your machine
* The executable was not properly compiled, or was compiled on a
different and incompatible environment.
* buggy compiler or libraries: this is the default explanation
if you have problems with the provided tests and examples.

P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone [phone], fax [phone]

[Paolo Giannozzi]

Post by Alexander Eftimiades
[debian:13270] [ 1] /usr/lib/libfftw3.so.3 [0xb6f30d5c]

if this message appears for all errors, compile internal
FFTW instead of using external FFTW v.3: in make.sys
replace -D__FFTW3 with -D__FFTW and remove -lfftw3
from libraries, delete all objects that depend upon such
options (rm Modules/fft_scalar.o clib/fft_stick.o should
be enough), recompile

P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone [phone], fax [phone]