Re: [Pw_forum] mpi error using pw.x

[Chong Wang]

Hi,

According to error messages, I think it is mpi that is broken, not ifort. Both 
versions are listed here:

ifort (IFORT) 16.0.3 20160415
Copyright (C) 1985-2016 Intel Corporation.  All rights reserved.
Intel(R) MPI Library for Linux* OS, Version 5.1.3 Build 20160120 (build id: 
14053)
Copyright (C) 2003-2016, Intel Corporation. All rights reserved.

Best!

Chong Wang


From: pw_forum-boun...@pwscf.org  on behalf of 
Filippo SPIGA 
Sent: Tuesday, May 17, 2016 1:59:16 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] mpi error using pw.x

On May 16, 2016, at 11:12 PM, Chong Wang  wrote:
> 1. With intel parallel studio 2016 update3, Errors in my original post 
> persists.

We had little compiler issue with Intel 16 in the past, I would not be 
surprised is somwthing else is broken. Which exact version of Intel IFORT you 
have?

Please run "ifort --version"

Thanks

--
Mr. Filippo SPIGA, M.Sc.
Quantum ESPRESSO Foundation
http://www.quantum-espresso.org ~ skype: filippo.spiga

*
Disclaimer: "Please note this message and any attachments are CONFIDENTIAL and 
may be privileged or otherwise protected from disclosure. The contents are not 
to be disclosed to anyone other than the addressee. Unauthorized recipients are 
requested to preserve this confidentiality and to advise the sender immediately 
of any error in transmission."


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Re: [Pw_forum] ESM Charge and Potential Output

[Marton]

Hi Nkosinathi,

In recent versions of Quantum Espresso these quantities are printed into a
file named prefix.esm1 (see also
http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#assume_isolated
).

HTH
Marton

--
Marton Voros
Materials Science Division
Argonne National Laboratory

On Mon, May 16, 2016 at 12:34 PM, Nkosinathi Malaza 
wrote:

> Dear All,
>
> I have a question, the output file using ESM does not print out the  ESM
> Charge and Potential in the output file. I have used it before and it used
> to print them out, has anything changed?
>
> Thanks
>
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Re: [Pw_forum] mpi error using pw.x

[Filippo SPIGA]

On May 16, 2016, at 11:12 PM, Chong Wang  wrote:
> 1. With intel parallel studio 2016 update3, Errors in my original post 
> persists.

We had little compiler issue with Intel 16 in the past, I would not be 
surprised is somwthing else is broken. Which exact version of Intel IFORT you 
have?

Please run "ifort --version"

Thanks

--
Mr. Filippo SPIGA, M.Sc.
Quantum ESPRESSO Foundation
http://www.quantum-espresso.org ~ skype: filippo.spiga

*
Disclaimer: "Please note this message and any attachments are CONFIDENTIAL and 
may be privileged or otherwise protected from disclosure. The contents are not 
to be disclosed to anyone other than the addressee. Unauthorized recipients are 
requested to preserve this confidentiality and to advise the sender immediately 
of any error in transmission."


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Re: [Pw_forum] ESM Charge and Potential Output

[Paolo Giannozzi]

Your chances to get an answer will increase from zero to a finite value (so
by an infinite factor) if you specify which versions you are referring to

On Mon, May 16, 2016 at 7:34 PM, Nkosinathi Malaza 
wrote:

> Dear All,
>
> I have a question, the output file using ESM does not print out the  ESM
> Charge and Potential in the output file. I have used it before and it used
> to print them out, has anything changed?
>
> Thanks
>
> ___
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> http://pwscf.org/mailman/listinfo/pw_forum
>



-- 
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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[Pw_forum] ESM Charge and Potential Output

[Nkosinathi Malaza]

Dear All,

I have a question, the output file using ESM does not print out the  ESM
Charge and Potential in the output file. I have used it before and it used
to print them out, has anything changed?

Thanks
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Re: [Pw_forum] mpi error using pw.x

[Chong Wang]

Hi Rolly:


Thank you for replying.


I was just looking for how to set mpi fortran compiler to mpiifort. ./configure 
-h shows how to set fortran compiler to ifort and c compiler to icc, but not 
mpi fortran compiler. Maybe developers can add some hints.


Progress:

1. With intel parallel studio 2016 update3, Errors in my original post persists.

2. With intel parallel studio 2015, Everything works well!


Cheers!


Chong Wang



From: pw_forum-boun...@pwscf.org  on behalf of 
Rolly Ng 
Sent: Monday, May 16, 2016 9:43 PM
To: PWSCF Forum
Subject: Re: [Pw_forum] mpi error using pw.x

Hi Chong Wang,

Perhaps it would be better to run ./configure with,
./configure CC=icc CXX=icpc F90=ifort F77=ifort MPIF90=mpiifort 
--with-scalapack=intel

so that QE knows which compiler to use, verified with QE v5.3.0.

Rolly

On 05/16/2016 05:52 PM, Paolo Giannozzi wrote:
On Mon, May 16, 2016 at 4:11 AM, Chong Wang 
> wrote:

I have checked my mpif90 calls gfortran so there's no mix up.

I am not sure it is possible to use gfortran together with intel mpi. If you 
have intel mpi and mkl, presumably you have the intel compiler as well.

Can you kindly share with me your make.sys?

it doesn't make sense to share a make.sys file unless the software 
configuration is the same.

Paolo


Thanks in advance!


Best!


Chong Wang


From: pw_forum-boun...@pwscf.org 
> on behalf of 
Paolo Giannozzi 
<p.gianno...@gmail.com>
Sent: Monday, May 16, 2016 3:10 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] mpi error using pw.x

Your make.sys shows clear signs of mixup between ifort and gfortran. Please 
verify that mpif90 calls ifort and not gfortran (or vice versa). Configure 
issues a warning if this happens.

I have successfully run your test on a machine with some recent intel compiler 
and intel mpi. The second output (run as mpirun -np 18 pw.x -nk 18) is an 
example of what I mean by "type of parallelization": there are many different 
parallelization levels in QE. This is on k-points (and runs faster in this case 
on less processors than parallelization on plane waves).

Paolo

On Sun, May 15, 2016 at 6:01 PM, Chong Wang 
> wrote:

Hi,


I have done more test:

1. intel mpi 2015 yields segment fault

2. intel mpi 2013 yields the same error here

Did I do something wrong with compiling? Here's my make.sys:


# make.sys.  Generated from make.sys.in by configure.


# compilation rules


.SUFFIXES :

.SUFFIXES : .o .c .f .f90


# most fortran compilers can directly preprocess c-like directives: use

# $(MPIF90) $(F90FLAGS) -c $<

# if explicit preprocessing by the C preprocessor is needed, use:

# $(CPP) $(CPPFLAGS) $< -o $*.F90

# $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o

# remember the tabulator in the first column !!!


.f90.o:

$(MPIF90) $(F90FLAGS) -c $<


# .f.o and .c.o: do not modify


.f.o:

$(F77) $(FFLAGS) -c $<


.c.o:

$(CC) $(CFLAGS)  -c $<




# Top QE directory, not used in QE but useful for linking QE libs with plugins

# The following syntax should always point to TOPDIR:

#   $(dir $(abspath $(filter %make.sys,$(MAKEFILE_LIST


TOPDIR = /home/wangc/temp/espresso-5.4.0


# DFLAGS  = precompilation options (possible arguments to -D and -U)

#   used by the C compiler and preprocessor

# FDFLAGS = as DFLAGS, for the f90 compiler

# See include/defs.h.README for a list of options and their meaning

# With the exception of IBM xlf, FDFLAGS = $(DFLAGS)

# For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas


# MANUAL_DFLAGS  = additional precompilation option(s), if desired

#  BEWARE: it does not work for IBM xlf! Manually edit FDFLAGS

MANUAL_DFLAGS  =

DFLAGS =  -D__GFORTRAN -D__STD_F95 -D__DFTI -D__MPI -D__PARA 
-D__SCALAPACK

FDFLAGS= $(DFLAGS) $(MANUAL_DFLAGS)


# IFLAGS = how to locate directories with *.h or *.f90 file to be included

#  typically -I../include -I/some/other/directory/

#  the latter contains .e.g. files needed by FFT libraries


IFLAGS = -I../include 
-I/opt/intel/compilers_and_libraries_2016.3.210/linux/mkl/include


# MOD_FLAGS = flag used by f90 compiler to locate modules

# Each Makefile defines the list of needed modules in MODFLAGS


MOD_FLAG  = -I


# Compilers: fortran-90, fortran-77, C

# If a parallel compilation is desired, MPIF90 should be a fortran-90

# compiler that produces executables for parallel execution using MPI

# (such as for instance mpif90, mpf90, mpxlf90,...);

# otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...)

# If you have a parallel machine but no suitable candidate for MPIF90,

# try 

Re: [Pw_forum] mpi error using pw.x

[Rolly Ng]

Hi Chong Wang,

Perhaps it would be better to run ./configure with,
./configure CC=icc CXX=icpc F90=ifort F77=ifort MPIF90=mpiifort 
--with-scalapack=intel


so that QE knows which compiler to use, verified with QE v5.3.0.

Rolly

On 05/16/2016 05:52 PM, Paolo Giannozzi wrote:
On Mon, May 16, 2016 at 4:11 AM, Chong Wang > wrote:


I have checked my mpif90 calls gfortran so there's no mix up.


I am not sure it is possible to use gfortran together with intel mpi. 
If you have intel mpi and mkl, presumably you have the intel compiler 
as well.


Can you kindly share with me your make.sys?


it doesn't make sense to share a make.sys file unless the software 
configuration is the same.


Paolo


Thanks in advance!


Best!


Chong Wang


*From:* pw_forum-boun...@pwscf.org
 > on behalf of Paolo Giannozzi
>
*Sent:* Monday, May 16, 2016 3:10 AM
*To:* PWSCF Forum
*Subject:* Re: [Pw_forum] mpi error using pw.x
Your make.sys shows clear signs of mixup between ifort and
gfortran. Please verify that mpif90 calls ifort and not gfortran
(or vice versa). Configure issues a warning if this happens.

I have successfully run your test on a machine with some recent
intel compiler and intel mpi. The second output (run as mpirun -np
18 pw.x -nk 18) is an example of what I mean by "type of
parallelization": there are many different parallelization levels
in QE. This is on k-points (and runs faster in this case on less
processors than parallelization on plane waves).

Paolo

On Sun, May 15, 2016 at 6:01 PM, Chong Wang > wrote:

Hi,


I have done more test:

1. intel mpi 2015 yields segment fault

2. intel mpi 2013 yields the same error here

Did I do something wrong with compiling? Here's my make.sys:


# make.sys.  Generated from make.sys.in 
by configure.


# compilation rules


.SUFFIXES :

.SUFFIXES : .o .c .f .f90


# most fortran compilers can directly preprocess c-like
directives: use

# $(MPIF90) $(F90FLAGS) -c $<

# if explicit preprocessing by the C preprocessor is needed, use:

# $(CPP) $(CPPFLAGS) $< -o $*.F90

#$(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o

# remember the tabulator in the first column !!!


.f90.o:

$(MPIF90) $(F90FLAGS) -c $<


# .f.o and .c.o: do not modify


.f.o:

$(F77) $(FFLAGS) -c $<


.c.o:

$(CC) $(CFLAGS) -c $<




# Top QE directory, not used in QE but useful for linking QE
libs with plugins

# The following syntax should always point to TOPDIR:

#   $(dir $(abspath $(filter %make.sys,$(MAKEFILE_LIST


TOPDIR = /home/wangc/temp/espresso-5.4.0


# DFLAGS  = precompilation options (possible arguments to -D
and -U)

#   used by the C compiler and preprocessor

# FDFLAGS = as DFLAGS, for the f90 compiler

# See include/defs.h.README for a list of options and their
meaning

# With the exception of IBM xlf, FDFLAGS = $(DFLAGS)

# For IBM xlf, FDFLAGS is the same as DFLAGS with separating
commas


# MANUAL_DFLAGS  = additional precompilation option(s), if desired

#  BEWARE: it does not work for IBM xlf!
Manually edit FDFLAGS

MANUAL_DFLAGS  =

DFLAGS =  -D__GFORTRAN -D__STD_F95 -D__DFTI -D__MPI
-D__PARA -D__SCALAPACK

FDFLAGS= $(DFLAGS) $(MANUAL_DFLAGS)


# IFLAGS = how to locate directories with *.h or *.f90 file to
be included

#  typically -I../include -I/some/other/directory/

#  the latter contains .e.g. files needed by FFT libraries


IFLAGS = -I../include
-I/opt/intel/compilers_and_libraries_2016.3.210/linux/mkl/include


# MOD_FLAGS = flag used by f90 compiler to locate modules

# Each Makefile defines the list of needed modules in MODFLAGS


MOD_FLAG  = -I


# Compilers: fortran-90, fortran-77, C

# If a parallel compilation is desired, MPIF90 should be a
fortran-90

# compiler that produces executables for parallel execution
using MPI

# (such as for instance mpif90, mpf90, mpxlf90,...);

# otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90,
ifort,...)

# If you have a parallel machine but no suitable candidate for
MPIF90,

# try to specify the directory 

[Pw_forum] sending the email address for posting

[Neha Bothra]

Hi,
   This is my email address- neha3bot...@gmail.com

Thank you,
Regards,
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Re: [Pw_forum] mpi error using pw.x

[Paolo Giannozzi]

On Mon, May 16, 2016 at 4:11 AM, Chong Wang  wrote:

I have checked my mpif90 calls gfortran so there's no mix up.
>

I am not sure it is possible to use gfortran together with intel mpi. If
you have intel mpi and mkl, presumably you have the intel compiler as well.


> Can you kindly share with me your make.sys?
>

it doesn't make sense to share a make.sys file unless the software
configuration is the same.

Paolo


Thanks in advance!
>
>
> Best!
>
>
> Chong Wang
> --
> *From:* pw_forum-boun...@pwscf.org  on behalf
> of Paolo Giannozzi 
> *Sent:* Monday, May 16, 2016 3:10 AM
> *To:* PWSCF Forum
> *Subject:* Re: [Pw_forum] mpi error using pw.x
>
> Your make.sys shows clear signs of mixup between ifort and gfortran.
> Please verify that mpif90 calls ifort and not gfortran (or vice versa).
> Configure issues a warning if this happens.
>
> I have successfully run your test on a machine with some recent intel
> compiler and intel mpi. The second output (run as mpirun -np 18 pw.x -nk
> 18) is an example of what I mean by "type of parallelization": there
> are many different parallelization levels in QE. This is on k-points (and
> runs faster in this case on less processors than parallelization on plane
> waves).
>
> Paolo
>
> On Sun, May 15, 2016 at 6:01 PM, Chong Wang  wrote:
>
>> Hi,
>>
>>
>> I have done more test:
>>
>> 1. intel mpi 2015 yields segment fault
>>
>> 2. intel mpi 2013 yields the same error here
>>
>> Did I do something wrong with compiling? Here's my make.sys:
>>
>>
>> # make.sys.  Generated from make.sys.in by configure.
>>
>>
>> # compilation rules
>>
>>
>> .SUFFIXES :
>>
>> .SUFFIXES : .o .c .f .f90
>>
>>
>> # most fortran compilers can directly preprocess c-like directives: use
>>
>> # $(MPIF90) $(F90FLAGS) -c $<
>>
>> # if explicit preprocessing by the C preprocessor is needed, use:
>>
>> # $(CPP) $(CPPFLAGS) $< -o $*.F90
>>
>> # $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o
>>
>> # remember the tabulator in the first column !!!
>>
>>
>> .f90.o:
>>
>> $(MPIF90) $(F90FLAGS) -c $<
>>
>>
>> # .f.o and .c.o: do not modify
>>
>>
>> .f.o:
>>
>> $(F77) $(FFLAGS) -c $<
>>
>>
>> .c.o:
>>
>> $(CC) $(CFLAGS)  -c $<
>>
>>
>>
>>
>> # Top QE directory, not used in QE but useful for linking QE libs with
>> plugins
>>
>> # The following syntax should always point to TOPDIR:
>>
>> #   $(dir $(abspath $(filter %make.sys,$(MAKEFILE_LIST
>>
>>
>> TOPDIR = /home/wangc/temp/espresso-5.4.0
>>
>>
>> # DFLAGS  = precompilation options (possible arguments to -D and -U)
>>
>> #   used by the C compiler and preprocessor
>>
>> # FDFLAGS = as DFLAGS, for the f90 compiler
>>
>> # See include/defs.h.README for a list of options and their meaning
>>
>> # With the exception of IBM xlf, FDFLAGS = $(DFLAGS)
>>
>> # For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas
>>
>>
>> # MANUAL_DFLAGS  = additional precompilation option(s), if desired
>>
>> #  BEWARE: it does not work for IBM xlf! Manually edit
>> FDFLAGS
>>
>> MANUAL_DFLAGS  =
>>
>> DFLAGS =  -D__GFORTRAN -D__STD_F95 -D__DFTI -D__MPI -D__PARA
>> -D__SCALAPACK
>>
>> FDFLAGS= $(DFLAGS) $(MANUAL_DFLAGS)
>>
>>
>> # IFLAGS = how to locate directories with *.h or *.f90 file to be included
>>
>> #  typically -I../include -I/some/other/directory/
>>
>> #  the latter contains .e.g. files needed by FFT libraries
>>
>>
>> IFLAGS = -I../include
>> -I/opt/intel/compilers_and_libraries_2016.3.210/linux/mkl/include
>>
>>
>> # MOD_FLAGS = flag used by f90 compiler to locate modules
>>
>> # Each Makefile defines the list of needed modules in MODFLAGS
>>
>>
>> MOD_FLAG  = -I
>>
>>
>> # Compilers: fortran-90, fortran-77, C
>>
>> # If a parallel compilation is desired, MPIF90 should be a fortran-90
>>
>> # compiler that produces executables for parallel execution using MPI
>>
>> # (such as for instance mpif90, mpf90, mpxlf90,...);
>>
>> # otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...)
>>
>> # If you have a parallel machine but no suitable candidate for MPIF90,
>>
>> # try to specify the directory containing "mpif.h" in IFLAGS
>>
>> # and to specify the location of MPI libraries in MPI_LIBS
>>
>>
>> MPIF90 = mpif90
>>
>> #F90   = gfortran
>>
>> CC = cc
>>
>> F77= gfortran
>>
>>
>> # C preprocessor and preprocessing flags - for explicit preprocessing,
>>
>> # if needed (see the compilation rules above)
>>
>> # preprocessing flags must include DFLAGS and IFLAGS
>>
>>
>> CPP= cpp
>>
>> CPPFLAGS   = -P -C -traditional $(DFLAGS) $(IFLAGS)
>>
>>
>> # compiler flags: C, F90, F77
>>
>> # C flags must include DFLAGS and IFLAGS
>>
>> # F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate
>> syntax
>>
>>
>> CFLAGS = -O3 $(DFLAGS) $(IFLAGS)
>>
>> F90FLAGS   = $(FFLAGS) -x f95-cpp-input