Re: [Pw_forum] How to do clean stop during running job
Dear Dr. Lorenzo Paulatto,
According to your suggestions, I got clean stop during running job.
Thanks again for your kind help.
On Fri, Oct 2, 2015 at 10:56 PM, Venkataramana Imandi <
venkataramana.ima...@gmail.com> wrote:
> Dear all,
>
> In the manual clean stop occurs as follows.
> 1. prefix.EXIT file is created in the execution directory.
> In my calculations, prefix.EXIT file is not created (prefix name given in
> the control namelist) during the calculations.
> If it is created in the execution directory, how to stop calculations
> (please suggest command prompt).
> 2. signal trapping
> add \mbox{"-D\_\_TERMINATE\_GRACEFULLY"} to \mbox{MANUAL\_DFLAGS} in the
> make.sys file for clean stop.
> But I don't know where and which position the above command add in the
> make.sys file (attached make.sys file) and please suggest me.
> I tried several ways with command as follows.
> qsig jobid
> qsig -s SIGTERM jobid
> qsig -s SIGTERM jobidname
>
> the above commands do not give clean stop, that means compilation is
> required with \mbox{"-D\_\_TERMINATE\_GRACEFULLY"} to \mbox{MANUAL\_DFLAGS}
> in the make.sys file.
> Please suggest, how to do clean stop in the QE calculations.
>
> make.sys file:
>
> # 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 $<
>
>
>
> # topdir for linking espresso libs with plugins
> TOPDIR = /soft/espresso-5.1.2-gnu
>
> # 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
> # You may use this instead of tweaking DFLAGS and FDFLAGS
> # BEWARE: will not work for IBM xlf! Manually edit FDFLAGS
> MANUAL_DFLAGS =
> DFLAGS = -D__GFORTRAN -D__STD_F95 -D__FFTW -D__MPI -D__PARA
> $(MANUAL_DFLAGS)
> FDFLAGS= $(DFLAGS) $(MANUAL_DFLAGS)
>
> # IFLAGS = how to locate directories where files to be included are
>
> # In most cases, IFLAGS = -I../include
>
> IFLAGS = -I../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 $(FDFLAGS) $(IFLAGS)
> $(MODFLAGS)
> FFLAGS = -O3 -g
>
> # compiler flags without optimization for fortran-77
> # the latter is NEEDED to properly compile dlamch.f, used by lapack
>
> FFLAGS_NOOPT = -O0 -g
>
> # compiler flag needed by some compilers when the main is not fortran
> # Currently used for YamboFFLAGS_NOMAIN =
>
> # Linker, linker-specific flags (if any)
> # Typically LD coincides with F90 or MPIF90, LD_LIBS is empty
>
> LD = mpif90
> LDFLAGS= -g -pthread
> LD_LIBS=
>
> # External Libraries (if any) : blas, lapack, fft, MPI
>
> # If you have nothing better, use the local copy :
> # BLAS_LIBS = /your/path/to/espresso/BLAS/blas.a
> # BLAS_LIBS_SWITCH = internal
>
> BLAS_LIBS = -lblas
> BLAS_LIBS_SWITCH = external
>
> # If you have nothing better, use the local copy :
> # LAPACK_LIBS =
Re: [Pw_forum] How to do clean stop during running job
On Friday, October 02, 2015 10:56:15 PM Venkataramana Imandi wrote:
> Dear all,
>
> In the manual clean stop occurs as follows.
> 1. prefix.EXIT file is created in the execution directory.
> In my calculations, prefix.EXIT file is not created (prefix name given in
> the control namelist) during the calculations.
It is not going to create itself, you have to create it if you want you want
to stop the code.
> 2. signal trapping
> add \mbox{"-D\_\_TERMINATE\_GRACEFULLY"} to \mbox{MANUAL\_DFLAGS} in the
> make.sys file for clean stop.
[ ...]
> But I don't know where and which position the above command add in the
> make.sys file (attached make.sys file) and please suggest me.
> # MANUAL_DFLAGS = additional precompilation option(s), if desired
> # You may use this instead of tweaking DFLAGS and FDFLAGS
> # BEWARE: will not work for IBM xlf! Manually edit FDFLAGS
> MANUAL_DFLAGS =
Here it is!
--
Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Université Paris 6
+33 (0)1 44 275 084 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/
23-24/4é16 Boîte courrier 115
4 place Jussieu 75252 Paris Cédex 05
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] How to do clean stop during running job
Dear all,
In the manual clean stop occurs as follows.
1. prefix.EXIT file is created in the execution directory.
In my calculations, prefix.EXIT file is not created (prefix name given in
the control namelist) during the calculations.
If it is created in the execution directory, how to stop calculations
(please suggest command prompt).
2. signal trapping
add \mbox{"-D\_\_TERMINATE\_GRACEFULLY"} to \mbox{MANUAL\_DFLAGS} in the
make.sys file for clean stop.
But I don't know where and which position the above command add in the
make.sys file (attached make.sys file) and please suggest me.
I tried several ways with command as follows.
qsig jobid
qsig -s SIGTERM jobid
qsig -s SIGTERM jobidname
the above commands do not give clean stop, that means compilation is
required with \mbox{"-D\_\_TERMINATE\_GRACEFULLY"} to \mbox{MANUAL\_DFLAGS}
in the make.sys file.
Please suggest, how to do clean stop in the QE calculations.
make.sys file:
# 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 $<
# topdir for linking espresso libs with plugins
TOPDIR = /soft/espresso-5.1.2-gnu
# 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
# You may use this instead of tweaking DFLAGS and FDFLAGS
# BEWARE: will not work for IBM xlf! Manually edit FDFLAGS
MANUAL_DFLAGS =
DFLAGS = -D__GFORTRAN -D__STD_F95 -D__FFTW -D__MPI -D__PARA
$(MANUAL_DFLAGS)
FDFLAGS= $(DFLAGS) $(MANUAL_DFLAGS)
# IFLAGS = how to locate directories where files to be included are
# In most cases, IFLAGS = -I../include
IFLAGS = -I../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 $(FDFLAGS) $(IFLAGS) $(MODFLAGS)
FFLAGS = -O3 -g
# compiler flags without optimization for fortran-77
# the latter is NEEDED to properly compile dlamch.f, used by lapack
FFLAGS_NOOPT = -O0 -g
# compiler flag needed by some compilers when the main is not fortran
# Currently used for YamboFFLAGS_NOMAIN =
# Linker, linker-specific flags (if any)
# Typically LD coincides with F90 or MPIF90, LD_LIBS is empty
LD = mpif90
LDFLAGS= -g -pthread
LD_LIBS=
# External Libraries (if any) : blas, lapack, fft, MPI
# If you have nothing better, use the local copy :
# BLAS_LIBS = /your/path/to/espresso/BLAS/blas.a
# BLAS_LIBS_SWITCH = internal
BLAS_LIBS = -lblas
BLAS_LIBS_SWITCH = external
# If you have nothing better, use the local copy :
# LAPACK_LIBS = /your/path/to/espresso/lapack-3.2/lapack.a
# LAPACK_LIBS_SWITCH = internal
# For IBM machines with essl (-D__ESSL): load essl BEFORE lapack !
# remember that LAPACK_LIBS precedes BLAS_LIBS in loading order
LAPACK_LIBS= -llapack -lblas
LAPACK_LIBS_SWITCH = external
ELPA_LIBS_SWITCH = disabled
SCALAPACK_LIBS =
# nothing needed here if the the internal copy of FFTW is compiled
# (needs -D__FFTW in DFLAGS)
FFT_LIBS =
# For parallel execution, the correct path to MPI libraries
