Error: Blacs setup failed. parameter 6 had an illegal value in function descinit in rdiag
I was compiling SIESTA (4.0.X) on a Xeon E5-2690 with the newest Intel Fortran compiler 18.0, mkl in parallel and intelmpi
When I am trying to run the example SiH in parallel, I encounter the following RUNTIME error when I try to run it on multiple processors:
outcell: Unit cell vectors (Ang):
10.860000 0.000000 0.000000
0.000000 10.860000 0.000000
0.000000 0.000000 10.860000
outcell: Cell vector modules (Ang) : 10.860000 10.860000 10.860000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 1280.8241
Gamma-point calculation with multiply-connected orbital pairs
Gamma-point calculation with multiply-connected orbital pairs
Folding of H and S implicitly performed
Folding of H and S implicitly performed
New_DM. Step: 1
Initializing Density Matrix...
iodm: Reading Density Matrix from files
Read DM has different structure. Fixing...
New grid distribution: 1
1 1: 24 1: 24 1: 12
2 1: 24 1: 24 13: 24
InitMesh: MESH = 48 x 48 x 48 = 110592
InitMesh: (bp) = 24 x 24 x 24 = 13824
InitMesh: Mesh cutoff (required, used) = 40.000 53.991 Ry
ExtMesh (bp) on 0 = 56 x 56 x 44 = 137984
New grid distribution: 2
1 1: 24 1: 24 1: 12
2 1: 24 1: 24 13: 24
New grid distribution: 3
1 1: 24 1: 24 1: 12
2 1: 24 1: 24 13: 24
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 56 x 56 x 44 = 137984
PhiOnMesh: Number of (b)points on node 0 = 6912
PhiOnMesh: nlist on node 0 = 201015
{ 0, 0}: On entry to { 0, 1}: On entry to
DESCINIT parameter number 6 had an illegal value
DERROR : Blacs setup has failed in rdiag!
ESCStopping Program from Node: 1
ERROR : Blacs setup has failed in rdiag!
Stopping Program from Node: 1
application called MPI_Abort(
What can be the cause of it?
Because the parameter in the specified function descinit in rdiag.f is hardcoded to 0.
What i have done so far was changing the optimization flag, but the error persists.
What I found out, is that it has to do with the Blacs process grid, but i don't know how to change the setting correctly.
Question information
- Language:
- English Edit question
- Status:
- Answered
- For:
- Siesta Edit question
- Assignee:
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- Last query:
- Last reply:
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Revision history for this message
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#1 |
Could you provide more information:
1) Siesta version
2) arch.make
3) return value of $(which mpirun) $(which mpiexec) from your compute nodes
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Revision history for this message
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#3 |
I code the same error on my local machine, when I tried to install it in parallel. I am using the newest version of the MKL and the Intel Compiler:
SIESTA version: 4.0.2
I am using the intel mpi compiler wrapper mpiifort for the compilation:
As I said before changing the optimization flags doesn't have an influence:
The MKL is linked statically.
arch.make file:
SIESTA_
FC=mpiifort
FFLAGS = -O2 -xHost -fp-model precise -prec-sqrt -prec-div \
-fimf-
-double-size 64 -real-size 32 \
-warn unused,
FFLAGS_SPECIAL= -O1 -xHost -ip -mp1 -fpp -heap-arrays 1024 -i4 \
-double-size 64 -real-size 32 \
-warn unused,
DUMMY_FOX=
FFLAGS_DEBUG=-g -O0 -debug full -traceback -C
LDFLAGS= -static-intel -static-libgcc
RANLIB=ranlib
FC_SERIAL=mpiifort
#
NETCDF_LIBS=
NETCDF_INTERFACE=
FPPFLAGS_CDF=
MPI_INTERFACE=
MKL_INCLUDE=
MPI_LIBS=
MKL_LIBS=
MPI_INCLUDE=
INCFLAGS=
#
FPPFLAGS_MPI=-DMPI -DMPI_TIMING -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DSIESTA__NO_MRRR
##
NETCDF_LIBS=
NETCDF_INTERFACE=
##
LIBS= $(MPI_LIB) -mkl=parallel \
${MKLROOT}
${MKLROOT}
-Wl,--start-group \
${MKLROOT}
${MKLROOT}
${MKLROOT}
${MKLROOT}
-Wl,--end-group -lstdc++ -lpthread -lm -ldl
#
SYS=nag
FPPFLAGS= $(FPPFLAGS_CDF) $(FPPFLAGS_MPI)
##
atom.o: atom.F
$(FC) -c $(FFLAGS_SPECIAL) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
state_analysis.o: state_analysis.F
$(FC) -c $(FFLAGS_SPECIAL) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
.F.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $<
.f.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $<
.F90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $<
.f90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $<
The ERROR CODE of the BLACS_GRIDINFO subroutine is: -6
http://
ERROR Code of mpirun:
PhiOnMesh: nlist on node 0 = 100450
[1] Gather(): algo #3 is selected
[2] Gather(): algo #3 is selected
[0] Gather(): algo #3 is selected
[3] Gather(): algo #3 is selected
[0] Allreduce(): algo #1 is selected
[1] Allreduce(): algo #1 is selected
[2] Allreduce(): algo #1 is selected
[3] Allreduce(): algo #1 is selected
[0] Allreduce(): algo #1 is selected
[1] Allreduce(): algo #1 is selected
[2] Allreduce(): algo #1 is selected
[3] Allreduce(): algo #1 is selected
[2] Allreduce(): algo #1 is selected
[3] Allreduce(): algo #1 is selected
[1] Allreduce(): algo #1 is selected
[0] Allreduce(): algo #1 is selected
[0] Allreduce(): algo #1 is selected
[1] Allreduce(): algo #1 is selected
[2] Allreduce(): algo #1 is selected
[3] Allreduce(): algo #1 is selected
[0] Allgather(): algo #1 is selected
[1] Allgather(): algo #1 is selected
[2] Allgather(): algo #1 is selected
[3] Allgather(): algo #1 is selected
[0] Allgather(): algo #1 is selected
[1] Allgather(): algo #1 is selected
[2] Allgather(): algo #1 is selected
[3] Allgather(): algo #1 is selected
[1] Allgather(): algo #1 is selected
[2] Allgather(): algo #1 is selected
[3] Allgather(): algo #1 is selected
[0] Allgather(): algo #1 is selected
[0] Allgather(): algo #1 is selected
[1] Allgather(): algo #1 is selected
[2] Allgather(): algo #1 is selected
[3] Allgather(): algo #1 is selected
[1] Allreduce(): algo #7 is selected
[2] Allreduce(): algo #7 is selected
[3] Allreduce(): algo #7 is selected
[0] Allreduce(): algo #7 is selected
[2] Allgather(): algo #1 is selected
[0] Allgather(): algo #1 is selected
[1] Allgather(): algo #1 is selected
[3] Allgather(): algo #1 is selected
[2] Allgather(): algo #1 is selected
[0] Allgather(): algo #1 is selected
[1] Allgather(): algo #1 is selected
[3] Allgather(): algo #1 is selected
[1] Allgather(): algo #1 is selected
[2] Allgather(): algo #1 is selected
[0] Allgather(): algo #1 is selected
[3] Allgather(): algo #1 is selected
[3] Allgather(): algo #1 is selected
[0] Allgather(): algo #1 is selected
[1] Allgather(): algo #1 is selected
[2] Allgather(): algo #1 is selected
[0] Allgather(): algo #1 is selected
[1] Allgather(): algo #1 is selected
[2] Allgather(): algo #1 is selected
[3] Allgather(): algo #1 is selected
[2] Allgather(): algo #1 is selected
[1] Allgather(): algo #1 is selected
[0] Allgather(): algo #1 is selected
[2] Allgather(): algo #1 is selected
[3] Allgather(): algo #1 is selected
[3] Allgather(): algo #1 is selected
[0] Allgather(): algo #1 is selected
[1] Allgather(): algo #1 is selected
[0] Allreduce(): algo #7 is selected
[3] Allreduce(): algo #7 is selected
[2] Allreduce(): algo #7 is selected
[1] Allreduce(): algo #7 is selected
[2] Allgather(): algo #1 is selected
[3] Allgather(): algo #1 is selected
[0] Allgather(): algo #1 is selected
[1] Allgather(): algo #1 is selected
[2] Allgather(): algo #1 is selected
[1] Allgather(): algo #1 is selected
[3] Allgather(): algo #1 is selected
[0] Allgather(): algo #1 is selected
[0] Allgather(): algo #1 is selected
[1] Allgather(): algo #1 is selected
[2] Allgather(): algo #1 is selected
[3] Allgather(): algo #1 is selected
[0] Allreduce(): algo #7 is selected
[3] Allreduce(): algo #7 is selected
[2] Allreduce(): algo #7 is selected
[1] Allreduce(): algo #7 is selected
[1] Allgather(): algo #1 is selected
[2] Allgather(): algo #1 is selected
[3] Allgather(): algo #1 is selected
[0] Allgather(): algo #1 is selected
[1] Allreduce(): algo #7 is selected
[2] Allreduce(): algo #7 is selected
[3] Allreduce(): algo #7 is selected
[0] Allreduce(): algo #7 is selected
[0] Allreduce(): algo #1 is selected
[1] Allreduce(): algo #1 is selected
[2] Allreduce(): algo #1 is selected
[3] Allreduce(): algo #1 is selected
[3] Bcast(): algo #8 is selected
[2] Bcast(): algo #8 is selected
[1] Bcast(): algo #8 is selected
[0] Bcast(): algo #8 is selected
[1] Allreduce(): algo #1 is selected
[2] Allreduce(): algo #1 is selected
[3] Allreduce(): algo #1 is selected
[0] Allreduce(): algo #1 is selected
[0] Allreduce(): algo #1 is selected
[3] Allreduce(): algo #1 is selected
[2] Allreduce(): algo #1 is selected
[1] Allreduce(): algo #1 is selected
[0] Allreduce(): algo #1 is selected
[1] Allreduce(): algo #1 is selected
[2] Allreduce(): algo #1 is selected
[2] Allreduce(): algo #1 is selected
[3] Allreduce(): algo #1 is selected
[3] Allreduce(): algo #1 is selected
[0] Allreduce(): algo #1 is selected
[1] Allreduce(): algo #1 is selected
[2] Allreduce(): algo #1 is selected
[0] Allreduce(): algo #1 is selected
[1] Allreduce(): algo #1 is selected
[3] Allreduce(): algo #1 is selected
[0] Allreduce(): algo #1 is selected
[1] Allreduce(): algo #1 is selected
[2] Allreduce(): algo #1 is selected
[3] Allreduce(): algo #1 is selected
[3] Allreduce(): algo #1 is selected
[0] Allreduce(): algo #1 is selected
[1] Allreduce(): algo #1 is selected
[2] Allreduce(): algo #1 is selected
[2] Allreduce(): algo #1 is selected
[0] Allreduce(): algo #1 is selected
[1] Allreduce(): algo #1 is selected
[3] Allreduce(): algo #1 is selected
{ 0, 0}: On entry to
D{ 0, 1}: On entry to
DESC{ 0, 2}: On entry to
DESCINIT parameter number 6 had an illegal value
{ 0, 3}: On entry to
DESCINIT parameter number 6 had an illegal value
ESCINIT parameter number 6 had an illegal value
INIT parameter number 6 had an illegal value
-6
ERROR : Blacs setup has failed in rdiag!
-6
-6
-6
Stopping Program from Node: 0
ERROR : Blacs setup has failed in rdiag!
Stopping Program from Node: 0
ERROR : Blacs setup has failed in rdiag!
ERROR : Blacs setup has failed in rdiag!
ERROR : Blacs setup has failed in rdiag!
application called MPI_Abort(
[proxy:
exitcode=1
[proxy:
[mpiexec@
Comment:
We are relying on the MKL because it provides also support for our Phi.
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Revision history for this message
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#4 |
I have never tried with the ILP64 libraries. I suspect these are the culprit.
You should probably use the LP64 libraries (that is what I have always used).
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Revision history for this message
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#5 |
I changed to LP64 now but:
PhiOnMesh: Number of (b)points on node 0 = 3456
PhiOnMesh: nlist on node 0 = 100450
0
0
0
0
{ 0, 0}: On entry to
PDSTEDC parameter number 10 had an illegal value
{ 0, 1}: On entry to
PDSTEDC parameter number 10 had an illegal value
{ 1, 0}: On entry to
PDSTEDC parameter number 10 had an illegal value
{ 1, 1}: On entry to
PDSTEDC parameter number 10 had an illegal value
Illegal argument to standard eigensolver
Stopping Program from Node: 0
Illegal argument to standard eigensolver
Stopping Program from Node: 0
Illegal argument to standard eigensolver
Illegal argument to standard eigensolver
Illegal argument to standard eigensolver
application called MPI_Abort(
[proxy:
exitcode=1
[proxy:
[mpiexec@
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Revision history for this message
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#6 |
Could you attach the full output
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Revision history for this message
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#7 |
Here it is the full output:
Intel(R) Parallel Studio XE 2018 Update 3 for Linux*
Copyright (C) 2009-2018 Intel Corporation. All rights reserved.
host: franco-X783X
=======
mpiexec options:
----------------
Base path: /opt/intel/
Launcher: ssh
Debug level: 1
Enable X: -1
Global environment:
-----
I_MPI_
LD_
LIBRARY_
LESSOPEN=| /usr/bin/lesspipe %s
I_MPI_
USER=franco
XDG_SEAT=seat0
SSH_
INTEL_
<email address hidden>
SHLVL=1
INTEL_
OLDPWD=
HOME=
MDM_
XDG_
DESKTOP_
QT_
ADVISOR_
IPPROOT=
QT_
GTK_
DAALROOT=
LC_
MPM_
GDM_
DBUS_
VT_
TBBROOT=
I_MPI_
CPLUS_
MDMSESSION=
I_MPI_
MANDATORY_
INFOPATH=
VT_
LOGNAME=franco
WINDOWID=
DESKTOP_
PSTLROOT=
VT_ARCH=intel64
_=/
DEFAULTS_
PKG_
XDG_
TERM=
GDBSERVER_
USERNAME=franco
GTK_
GNOME_
I_MPI_
WINDOWPATH=7
PATH=
CLCK_
SESSION_
LC_
XDG_
INSPECTOR_
LC_
LANG=
XDG_
LS_
XDG_
XAUTHORITY=
SSH_
SHELL=/bin/bash
LC_
QT_
GDMSESSION=
MKLROOT=
VT_
LESSCLOSE=
LC_
I_MPI_
NLSPATH=
LC_
I_MPI_DEBUG=10
CLASSPATH=
XDG_VTNR=7
PWD=
VTUNE_
XDG_
I_MPI_
VT_
XDG_
LC_
MDM_
PYTHONPATH=
I_MPI_
LC_
CPATH=
GDB_
MANPATH=
VTE_
VT_MPI=impi4
Hydra internal environment:
-----
MPIR_
GFORTRAN_
I_MPI_
DAPL_
Intel(R) MPI Library specific variables:
-----
I_MPI_
I_MPI_
I_MPI_
I_MPI_
I_MPI_
I_MPI_
I_MPI_DEBUG=10
I_MPI_
I_MPI_
I_MPI_
Proxy information:
***
[1] proxy: franco-X783X (4 cores)
Exec list: ../../Obj/siesta (4 processes);
=======
[mpiexec@
[mpiexec@
Proxy launch args: /opt/intel/
Arguments being passed to proxy 0:
--version 3.2 --iface-ip-env-name MPIR_CVAR_
[mpiexec@
[proxy:
[proxy:
[proxy:
pmi_version=1 pmi_subversion=1
[proxy:
[proxy:
pmi_version=1 pmi_subversion=1
[proxy:
[proxy:
pmi_version=1 pmi_subversion=1
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
pmi_version=1 pmi_subversion=1
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[mpiexec@
[mpiexec@
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
12 franco-X783X 0,1,2,3,
[proxy:
[proxy:
12 franco-X783X 0,1,2,3,
[proxy:
[proxy:
12 franco-X783X 0,1,2,3,
[proxy:
[proxy:
[proxy:
[proxy:
12 franco-X783X 0,1,2,3,
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
Intel(R) MPI Library, Version 2018 Update 3 Build 20180411 (id: 18329)
Copyright (C) 2003-2018 Intel Corporation. All rights reserved.
[0] MPI startup(): Intel(R) MPI Library, Version 2018 Update 3 Build 20180411 (id: 18329)
[0] MPI startup(): Copyright (C) 2003-2018 Intel Corporation. All rights reserved.
[0] MPI startup(): Multi-threaded optimized library
[proxy:
[proxy:
[proxy:
[proxy:
kvsname=kvs_25579_0 key=sharedFilen
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[mpiexec@
[mpiexec@
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
kvsname=kvs_25579_0 key=sharedFilen
[proxy:
[proxy:
kvsname=kvs_25579_0 key=sharedFilen
[proxy:
[proxy:
kvsname=kvs_25579_0 key=sharedFilen
[proxy:
[proxy:
kvsname=kvs_25579_0 key=P0-
[proxy:
[proxy:
kvsname=kvs_25579_0 key=P1-
[proxy:
[proxy:
kvsname=kvs_25579_0 key=P2-
[proxy:
[proxy:
kvsname=kvs_25579_0 key=P3-
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[proxy:
[0] MPI startup(): shm data transfer mode
[1] MPI startup(): shm data transfer mode
[2] MPI startup(): shm data transfer mode
[3] MPI startup(): shm data transfer mode
[mpiexec@
[mpiexec@
[mpiexec@
[mpiexec@
[mpiexec@
[mpiexec@
[proxy:
[proxy:
[proxy:
[proxy:
[0] MPI startup(): Device_reset_idx=8
[0] MPI startup(): Allgather: 3: 0-0 & 0-2147483647
[0] MPI startup(): Allgather: 1: 1-6459 & 0-2147483647
[0] MPI startup(): Allgather: 5: 6460-14628 & 0-2147483647
[0] MPI startup(): Allgather: 1: 14629-25466 & 0-2147483647
[0] MPI startup(): Allgather: 3: 25467-36131 & 0-2147483647
[0] MPI startup(): Allgather: 5: 0-2147483647 & 0-2147483647
[0] MPI startup(): Allgatherv: 1: 0-7199 & 0-2147483647
[0] MPI startup(): Allgatherv: 3: 0-2147483647 & 0-2147483647
[0] MPI startup(): Allreduce: 7: 0-4 & 0-2147483647
[0] MPI startup(): Allreduce: 1: 5-8 & 0-2147483647
[0] MPI startup(): Allreduce: 7: 9-32 & 0-2147483647
[0] MPI startup(): Allreduce: 1: 33-64 & 0-2147483647
[0] MPI startup(): Allreduce: 7: 65-341 & 0-2147483647
[0] MPI startup(): Allreduce: 1: 342-6656 & 0-2147483647
[0] MPI startup(): Allreduce: 7: 6657-8192 & 0-2147483647
[0] MPI startup(): Allreduce: 2: 8193-113595 & 0-2147483647
[0] MPI startup(): Allreduce: 7: 113596-132320 & 0-2147483647
[0] MPI startup(): Allreduce: 2: 132321-1318322 & 0-2147483647
[0] MPI startup(): Allreduce: 7: 0-2147483647 & 0-2147483647
[0] MPI startup(): Alltoall: 3: 0-25 & 0-2147483647
[0] MPI startup(): Alltoall: 4: 26-37 & 0-2147483647
[0] MPI startup(): Alltoall: 3: 38-1024 & 0-2147483647
[0] MPI startup(): Alltoall: 4: 1025-4096 & 0-2147483647
[0] MPI startup(): Alltoall: 2: 4097-70577 & 0-2147483647
[0] MPI startup(): Alltoall: 4: 0-2147483647 & 0-2147483647
[0] MPI startup(): Alltoallv: 1: 0-2147483647 & 0-2147483647
[0] MPI startup(): Alltoallw: 0: 0-2147483647 & 0-2147483647
[0] MPI startup(): Barrier: 2: 0-2147483647 & 0-2147483647
[0] MPI startup(): Bcast: 1: 0-0 & 0-2147483647
[0] MPI startup(): Bcast: 8: 1-12746 & 0-2147483647
[0] MPI startup(): Bcast: 1: 12747-42366 & 0-2147483647
[0] MPI startup(): Bcast: 7: 0-2147483647 & 0-2147483647
[0] MPI startup(): Exscan: 0: 0-2147483647 & 0-2147483647
[0] MPI startup(): Gather: 1: 0-0 & 0-2147483647
[0] MPI startup(): Gather: 3: 0-2147483647 & 0-2147483647
[0] MPI startup(): Gatherv: 1: 0-2147483647 & 0-2147483647
[0] MPI startup(): Reduce_scatter: 4: 0-5 & 0-2147483647
[0] MPI startup(): Reduce_scatter: 1: 6-128 & 0-2147483647
[0] MPI startup(): Reduce_scatter: 3: 129-89367 & 0-2147483647
[0] MPI startup(): Reduce_scatter: 2: 0-2147483647 & 0-2147483647
[0] MPI startup(): Reduce: 1: 0-0 & 0-2147483647
[0] MPI startup(): Reduce: 7: 1-39679 & 0-2147483647
[0] MPI startup(): Reduce: 1: 0-2147483647 & 0-2147483647
[0] MPI startup(): Scan: 0: 0-2147483647 & 0-2147483647
[0] MPI startup(): Scatter: 1: 0-0 & 0-2147483647
[0] MPI startup(): Scatter: 3: 0-2147483647 & 0-2147483647
[0] MPI startup(): Scatterv: 0: 0-2147483647 & 0-2147483647
[1] MPI startup(): Recognition=2 Platform(code=32 ippn=2 dev=1) Fabric(intra=1 inter=1 flags=0x0)
[2] MPI startup(): Recognition=2 Platform(code=32 ippn=2 dev=1) Fabric(intra=1 inter=1 flags=0x0)
[0] MPI startup(): Rank Pid Node name Pin cpu
[3] MPI startup(): Recognition=2 Platform(code=32 ippn=2 dev=1) Fabric(intra=1 inter=1 flags=0x0)
[0] MPI startup(): 0 25584 franco-X783X 0
[0] MPI startup(): 1 25585 franco-X783X 1
[0] MPI startup(): 2 25586 franco-X783X 2
[0] MPI startup(): 3 25587 franco-X783X 3
[0] MPI startup(): Recognition=2 Platform(code=32 ippn=2 dev=1) Fabric(intra=1 inter=1 flags=0x0)
[0] MPI startup(): I_MPI_DEBUG=10
[0] MPI startup(): I_MPI_INFO_
[0] MPI startup(): I_MPI_INFO_
[0] MPI startup(): I_MPI_INFO_
[0] MPI startup(): I_MPI_INFO_
[0] MPI startup(): I_MPI_INFO_CACHES=3
[0] MPI startup(): I_MPI_INFO_
[0] MPI startup(): I_MPI_INFO_
[0] MPI startup(): I_MPI_INFO_
[0] MPI startup(): I_MPI_INFO_
[0] MPI startup(): I_MPI_INFO_
[0] MPI startup(): I_MPI_INFO_
[0] MPI startup(): I_MPI_INFO_
[0] MPI startup(): I_MPI_INFO_
[0] MPI startup(): I_MPI_INFO_
[0] MPI startup(): I_MPI_INFO_
[0] MPI startup(): I_MPI_INFO_LCPU=8
[0] MPI startup(): I_MPI_INFO_MODE=775
[0] MPI startup(): I_MPI_INFO_
[0] MPI startup(): I_MPI_INFO_
[0] MPI startup(): I_MPI_INFO_
[0] MPI startup(): I_MPI_INFO_STATE=0
[0] MPI startup(): I_MPI_INFO_
[0] MPI startup(): I_MPI_INFO_VEND=1
[0] MPI startup(): I_MPI_PIN_INFO=0
[0] MPI startup(): I_MPI_PIN_
[0] MPI startup(): I_MPI_PRINT_
[0] MPI startup(): I_MPI_SHM_LMT=shm
Siesta Version : SIESTA_VERSION
Architecture : SIESTA_ARCH
Compiler version: COMPILER_VERSION
Compiler flags : FFLAGS
PP flags : FPPFLAGS
PARALLEL version
* Running on 4 nodes in parallel
>> Start of run: 10-SEP-2018 18:24:33
reinit: Reading from standard input
*******
# $Id: sih.fdf,v 1.1 1999/04/20 14:43:44 emilio Exp $
# -------
# FDF for interstitial H in a cubic c-Si supercell with 64 atoms
#
# E. Artacho, April 1999
# -------
SystemName H in 64-atom silicon
SystemLabel sih
NumberOfAtoms 65
NumberOfSpecies 2
%block ChemicalSpecies
1 14 Si
2 1 H
%endblock ChemicalSpecies
PAO.BasisSize SZ
PAO.EnergyShift 300 meV
%block PAO.Basis
H 1
0 1
0.
0.8
%endblock PAO.Basis
LatticeConstant 5.430 Ang
%block LatticeVectors
2.000 0.000 0.000
0.000 2.000 0.000
0.000 0.000 2.000
%endblock LatticeVectors
MeshCutoff 40.0 Ry
MaxSCFIterations 50
DM.MixingWeight 0.3
DM.NumberPulay 3
DM.Tolerance 1.d-3
DM.UseSaveDM
SolutionMethod diagon
ElectronicTempe
MD.TypeOfRun cg
MD.NumCGsteps 100
MD.MaxCGDispl 0.01 Ang
MD.MaxForceTol 0.005 eV/Ang
AtomicCoordinat
%block AtomicCoordinat
0.000 0.000 0.000 1 # Si 1
0.250 0.250 0.250 1 # Si 2
0.000 0.500 0.500 1 # Si 3
0.250 0.750 0.750 1 # Si 4
0.500 0.000 0.500 1 # Si 5
0.750 0.250 0.750 1 # Si 6
0.500 0.500 0.000 1 # Si 7
0.750 0.750 0.250 1 # Si 8
1.000 0.000 0.000 1 # Si 9
1.250 0.250 0.250 1 # Si 10
1.000 0.500 0.500 1 # Si 11
1.250 0.750 0.750 1 # Si 12
1.500 0.000 0.500 1 # Si 13
1.750 0.250 0.750 1 # Si 14
1.500 0.500 0.000 1 # Si 15
1.750 0.750 0.250 1 # Si 16
0.000 1.000 0.000 1 # Si 17
0.250 1.250 0.250 1 # Si 18
0.000 1.500 0.500 1 # Si 19
0.250 1.750 0.750 1 # Si 20
0.500 1.000 0.500 1 # Si 21
0.750 1.250 0.750 1 # Si 22
0.500 1.500 0.000 1 # Si 23
0.750 1.750 0.250 1 # Si 24
0.000 0.000 1.000 1 # Si 25
0.250 0.250 1.250 1 # Si 26
0.000 0.500 1.500 1 # Si 27
0.250 0.750 1.750 1 # Si 28
0.500 0.000 1.500 1 # Si 29
0.750 0.250 1.750 1 # Si 30
0.500 0.500 1.000 1 # Si 31
0.750 0.750 1.250 1 # Si 32
1.000 1.000 0.000 1 # Si 33
1.250 1.250 0.250 1 # Si 34
1.000 1.500 0.500 1 # Si 35
1.250 1.750 0.750 1 # Si 36
1.500 1.000 0.500 1 # Si 37
1.750 1.250 0.750 1 # Si 38
1.500 1.500 0.000 1 # Si 39
1.750 1.750 0.250 1 # Si 40
1.000 0.000 1.000 1 # Si 41
1.250 0.250 1.250 1 # Si 42
1.000 0.500 1.500 1 # Si 43
1.250 0.750 1.750 1 # Si 44
1.500 0.000 1.500 1 # Si 45
1.750 0.250 1.750 1 # Si 46
1.500 0.500 1.000 1 # Si 47
1.750 0.750 1.250 1 # Si 48
0.000 1.000 1.000 1 # Si 49
0.250 1.250 1.250 1 # Si 50
0.000 1.500 1.500 1 # Si 51
0.250 1.750 1.750 1 # Si 52
0.500 1.000 1.500 1 # Si 53
0.750 1.250 1.750 1 # Si 54
0.500 1.500 1.000 1 # Si 55
0.750 1.750 1.250 1 # Si 56
1.000 1.000 1.000 1 # Si 57
1.250 1.250 1.250 1 # Si 58
1.000 1.500 1.500 1 # Si 59
1.250 1.750 1.750 1 # Si 60
1.500 1.000 1.500 1 # Si 61
1.750 1.250 1.750 1 # Si 62
1.500 1.500 1.000 1 # Si 63
1.750 1.750 1.250 1 # Si 64
1.125 1.125 1.125 2 # H 65
%endblock AtomicCoordinat
*******
reinit: -------
reinit: System Name: H in 64-atom silicon
reinit: -------
reinit: System Label: sih
reinit: -------
initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Species number: 1 Label: Si Atomic number: 14
Species number: 2 Label: H Atomic number: 1
Ground state valence configuration: 3s02 3p02
Reading pseudopotential information in formatted form from Si.psf
Valence configuration for pseudopotential generation:
3s( 2.00) rc: 1.89
3p( 2.00) rc: 1.89
3d( 0.00) rc: 1.89
4f( 0.00) rc: 1.89
Ground state valence configuration: 1s01
Reading pseudopotential information in formatted form from H.psf
Valence configuration for pseudopotential generation:
1s( 1.00) rc: 1.25
2p( 0.00) rc: 1.25
3d( 0.00) rc: 1.25
4f( 0.00) rc: 1.25
For Si, standard SIESTA heuristics set lmxkb to 2
(one more than the basis l, including polarization orbitals).
Use PS.lmax or PS.KBprojectors blocks to override.
For H, standard SIESTA heuristics set lmxkb to 1
(one more than the basis l, including polarization orbitals).
Use PS.lmax or PS.KBprojectors blocks to override.
<basis_specs>
=======
Si Z= 14 Mass= 28.090 Charge= 0.17977+309
Lmxo=1 Lmxkb= 2 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=3
n=1 nzeta=1 polorb=0
L=1 Nsemic=0 Cnfigmx=3
n=1 nzeta=1 polorb=0
-------
L=0 Nkbl=1 erefs: 0.17977+309
L=1 Nkbl=1 erefs: 0.17977+309
L=2 Nkbl=1 erefs: 0.17977+309
=======
</basis_specs>
atom: Called for Si (Z = 14)
read_vps: Pseudopotential generation method:
read_vps: ATM3 Troullier-Martins
Total valence charge: 4.00000
xc_check: Exchange-
xc_check: Ceperley-Alder
V l=0 = -2*Zval/r beyond r= 2.5494
V l=1 = -2*Zval/r beyond r= 2.5494
V l=2 = -2*Zval/r beyond r= 2.5494
All V_l potentials equal beyond r= 1.8652
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r= 2.5494
Using large-core scheme for Vlocal
atom: Estimated core radius 2.54944
atom: Including non-local core corrections could be a good idea
atom: Maximum radius for 4*pi*r*
atom: Maximum radius for r*vlocal+2*Zval: 2.58151
GHOST: No ghost state for L = 0
GHOST: No ghost state for L = 1
GHOST: No ghost state for L = 2
KBgen: Kleinman-Bylander projectors:
l= 0 rc= 1.936440 el= -0.796617 Ekb= 4.661340 kbcos= 0.299756
l= 1 rc= 1.936440 el= -0.307040 Ekb= 1.494238 kbcos= 0.301471
l= 2 rc= 1.936440 el= 0.002313 Ekb= -2.808672 kbcos= -0.054903
KBgen: Total number of Kleinman-Bylander projectors: 9
atom: -------
atom: SANKEY-TYPE ORBITALS:
SPLIT: Orbitals with angular momentum L= 0
SPLIT: Basis orbitals for state 3s
SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.022049 Ry
izeta = 1
potential(
SPLIT: Orbitals with angular momentum L= 1
SPLIT: Basis orbitals for state 3p
SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.022049 Ry
izeta = 1
potential(
atom: Total number of Sankey-type orbitals: 4
atm_pop: Valence configuration (for local Pseudopot. screening):
3s( 2.00)
3p( 2.00)
Vna: chval, zval: 4.00000 4.00000
Vna: Cut-off radius for the neutral-atom potential: 6.116033
atom: _______
<basis_specs>
=======
H Z= 1 Mass= 1.0100 Charge= 0.17977+309
Lmxo=0 Lmxkb= 1 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=1
n=1 nzeta=1 polorb=0
-------
L=0 Nkbl=1 erefs: 0.17977+309
L=1 Nkbl=1 erefs: 0.17977+309
=======
</basis_specs>
atom: Called for H (Z = 1)
read_vps: Pseudopotential generation method:
read_vps: ATM3 Troullier-Martins
Total valence charge: 1.00000
xc_check: Exchange-
xc_check: Ceperley-Alder
V l=0 = -2*Zval/r beyond r= 1.2343
V l=1 = -2*Zval/r beyond r= 1.2189
All V_l potentials equal beyond r= 1.2343
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r= 1.2343
VLOCAL1: 99.0% of the norm of Vloc inside 28.493 Ry
VLOCAL1: 99.9% of the norm of Vloc inside 64.935 Ry
atom: Maximum radius for 4*pi*r*
atom: Maximum radius for r*vlocal+2*Zval: 1.21892
GHOST: No ghost state for L = 0
GHOST: No ghost state for L = 1
KBgen: Kleinman-Bylander projectors:
l= 0 rc= 1.364359 el= -0.467325 Ekb= -2.005361 kbcos= -0.336422
l= 1 rc= 1.434438 el= 0.001430 Ekb= -0.501708 kbcos= -0.021697
KBgen: Total number of Kleinman-Bylander projectors: 4
atom: -------
atom: SANKEY-TYPE ORBITALS:
SPLIT: Orbitals with angular momentum L= 0
SPLIT: Basis orbitals for state 1s
SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.022049 Ry
izeta = 1
potential(
atom: Total number of Sankey-type orbitals: 1
atm_pop: Valence configuration (for local Pseudopot. screening):
1s( 1.00)
Vna: chval, zval: 1.00000 1.00000
Vna: Cut-off radius for the neutral-atom potential: 4.708991
atom: _______
prinput: Basis input -------
PAO.BasisType split
%block ChemicalSpecies
1 14 Si # Species index, atomic number, species label
2 1 H # Species index, atomic number, species label
%endblock ChemicalSpecies
%block PAO.Basis # Define Basis set
Si 2 # Species label, number of l-shells
n=3 0 1 # n, l, Nzeta
4.884
1.000
n=3 1 1 # n, l, Nzeta
6.116
1.000
H 1 # Species label, number of l-shells
n=1 0 1 # n, l, Nzeta
4.718
0.800
%endblock PAO.Basis
prinput: -------
coor: Atomic-coordinates input format = Cartesian coordinates
coor: (in units of alat)
siesta: Atomic coordinates (Bohr) and species
siesta: 0.00000 0.00000 0.00000 1 1
siesta: 2.56530 2.56530 2.56530 1 2
siesta: 0.00000 5.13061 5.13061 1 3
siesta: 2.56530 7.69591 7.69591 1 4
siesta: 5.13061 0.00000 5.13061 1 5
siesta: 7.69591 2.56530 7.69591 1 6
siesta: 5.13061 5.13061 0.00000 1 7
siesta: 7.69591 7.69591 2.56530 1 8
siesta: 10.26122 0.00000 0.00000 1 9
siesta: 12.82652 2.56530 2.56530 1 10
siesta: 10.26122 5.13061 5.13061 1 11
siesta: 12.82652 7.69591 7.69591 1 12
siesta: 15.39183 0.00000 5.13061 1 13
siesta: 17.95713 2.56530 7.69591 1 14
siesta: 15.39183 5.13061 0.00000 1 15
siesta: 17.95713 7.69591 2.56530 1 16
siesta: 0.00000 10.26122 0.00000 1 17
siesta: 2.56530 12.82652 2.56530 1 18
siesta: 0.00000 15.39183 5.13061 1 19
siesta: 2.56530 17.95713 7.69591 1 20
siesta: 5.13061 10.26122 5.13061 1 21
siesta: 7.69591 12.82652 7.69591 1 22
siesta: 5.13061 15.39183 0.00000 1 23
siesta: 7.69591 17.95713 2.56530 1 24
siesta: 0.00000 0.00000 10.26122 1 25
siesta: 2.56530 2.56530 12.82652 1 26
siesta: 0.00000 5.13061 15.39183 1 27
siesta: 2.56530 7.69591 17.95713 1 28
siesta: 5.13061 0.00000 15.39183 1 29
siesta: 7.69591 2.56530 17.95713 1 30
siesta: 5.13061 5.13061 10.26122 1 31
siesta: 7.69591 7.69591 12.82652 1 32
siesta: 10.26122 10.26122 0.00000 1 33
siesta: 12.82652 12.82652 2.56530 1 34
siesta: 10.26122 15.39183 5.13061 1 35
siesta: 12.82652 17.95713 7.69591 1 36
siesta: 15.39183 10.26122 5.13061 1 37
siesta: 17.95713 12.82652 7.69591 1 38
siesta: 15.39183 15.39183 0.00000 1 39
siesta: 17.95713 17.95713 2.56530 1 40
siesta: 10.26122 0.00000 10.26122 1 41
siesta: 12.82652 2.56530 12.82652 1 42
siesta: 10.26122 5.13061 15.39183 1 43
siesta: 12.82652 7.69591 17.95713 1 44
siesta: 15.39183 0.00000 15.39183 1 45
siesta: 17.95713 2.56530 17.95713 1 46
siesta: 15.39183 5.13061 10.26122 1 47
siesta: 17.95713 7.69591 12.82652 1 48
siesta: 0.00000 10.26122 10.26122 1 49
siesta: 2.56530 12.82652 12.82652 1 50
siesta: 0.00000 15.39183 15.39183 1 51
siesta: 2.56530 17.95713 17.95713 1 52
siesta: 5.13061 10.26122 15.39183 1 53
siesta: 7.69591 12.82652 17.95713 1 54
siesta: 5.13061 15.39183 10.26122 1 55
siesta: 7.69591 17.95713 12.82652 1 56
siesta: 10.26122 10.26122 10.26122 1 57
siesta: 12.82652 12.82652 12.82652 1 58
siesta: 10.26122 15.39183 15.39183 1 59
siesta: 12.82652 17.95713 17.95713 1 60
siesta: 15.39183 10.26122 15.39183 1 61
siesta: 17.95713 12.82652 17.95713 1 62
siesta: 15.39183 15.39183 10.26122 1 63
siesta: 17.95713 17.95713 12.82652 1 64
siesta: 11.54387 11.54387 11.54387 2 65
siesta: System type = bulk
initatomlists: Number of atoms, orbitals, and projectors: 65 257 580
siesta: *******
siesta:
siesta: The following are some of the parameters of the simulation.
siesta: A complete list of the parameters used, including default values,
siesta: can be found in file out.fdf
siesta:
redata: Non-Collinear-spin run = F
redata: SpinPolarized (Up/Down) run = F
redata: Number of spin components = 1
redata: Long output = F
redata: Number of Atomic Species = 2
redata: Charge density info will appear in .RHO file
redata: Write Mulliken Pop. = NO
redata: Matel table size (NRTAB) = 1024
redata: Mesh Cutoff = 40.0000 Ry
redata: Net charge of the system = 0.0000 |e|
redata: Min. number of SCF Iter = 0
redata: Max. number of SCF Iter = 50
redata: Mix DM or H after convergence = F
redata: Recompute H after scf cycle = F
redata: Performing Pulay mixing using = 3 iterations
redata: Mix DM in first SCF step ? = F
redata: Write Pulay info on disk? = F
redata: Discard 1st Pulay DM after kick = F
redata: New DM Mixing Weight = 0.3000
redata: New DM Occupancy tolerance = 0.000000000001
redata: No kicks to SCF
redata: DM Mixing Weight for Kicks = 0.5000
redata: DM Tolerance for SCF = 0.001000
redata: Require (free) Energy convergence in SCF = F
redata: DM (free)Energy tolerance for SCF = 0.000010 eV
redata: Require Harris convergence for SCF = F
redata: DM Harris energy tolerance for SCF = 0.000010 eV
redata: Using Saved Data (generic) = F
redata: Use continuation files for DM = T
redata: Neglect nonoverlap interactions = F
redata: Method of Calculation = Diagonalization
redata: Divide and Conquer = T
redata: Electronic Temperature = 0.0018 Ry
redata: Fix the spin of the system = F
redata: Dynamics option = CG coord. optimization
redata: Variable cell = F
redata: Use continuation files for CG = F
redata: Max atomic displ per move = 0.0189 Bohr
redata: Maximum number of CG moves = 100
redata: Force tolerance = 0.0002 Ry/Bohr
redata: *******
Total number of electrons: 257.000000
Total ionic charge: 257.000000
* ProcessorY, Blocksize: 2 24
* Orbital distribution balance (max,min): 72 48
Kpoints in: 1 . Kpoints trimmed: 1
siesta: k-grid: Number of k-points = 1
siesta: k-grid: Cutoff (effective) = 5.430 Ang
siesta: k-grid: Supercell and displacements
siesta: k-grid: 1 0 0 0.000
siesta: k-grid: 0 1 0 0.000
siesta: k-grid: 0 0 1 0.000
outcell: Unit cell vectors (Ang):
10.860000 0.000000 0.000000
0.000000 10.860000 0.000000
0.000000 0.000000 10.860000
outcell: Cell vector modules (Ang) : 10.860000 10.860000 10.860000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 1280.8241
Gamma-point calculation with multiply-connected orbital pairs
Gamma-point calculation with multiply-connected orbital pairs
Folding of H and S implicitly performed
Folding of H and S implicitly performed
New_DM. Step: 1
Initializing Density Matrix...
New grid distribution: 1
1 1: 24 1: 12 1: 12
2 1: 24 1: 12 13: 24
3 1: 24 13: 24 1: 12
4 1: 24 13: 24 13: 24
InitMesh: MESH = 48 x 48 x 48 = 110592
InitMesh: (bp) = 24 x 24 x 24 = 13824
InitMesh: Mesh cutoff (required, used) = 40.000 53.991 Ry
ExtMesh (bp) on 0 = 56 x 44 x 44 = 108416
New grid distribution: 2
1 1: 24 1: 12 1: 12
2 1: 24 1: 12 13: 24
3 1: 24 13: 24 1: 12
4 1: 24 13: 24 13: 24
New grid distribution: 3
1 1: 24 1: 12 1: 12
2 1: 24 1: 12 13: 24
3 1: 24 13: 24 1: 12
4 1: 24 13: 24 13: 24
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 56 x 44 x 44 = 108416
PhiOnMesh: Number of (b)points on node 0 = 3456
PhiOnMesh: nlist on node 0 = 100450
0
0
0
0
{ 0, 0}: On entry to
PDSTEDC parameter number 10 had an illegal value
{ 0, 1}: On entry to
PDSTEDC parameter number 10 had an illegal value
{ 1, 0}: On entry to
PDSTEDC parameter number 10 had an illegal value
{ 1, 1}: On entry to
PDSTEDC parameter number 10 had an illegal value
Illegal argument to standard eigensolver
Stopping Program from Node: 0
Illegal argument to standard eigensolver
Stopping Program from Node: 0
Illegal argument to standard eigensolver
Illegal argument to standard eigensolver
Illegal argument to standard eigensolver
application called MPI_Abort(
[proxy:
exitcode=1
[proxy:
[mpiexec@
|
Revision history for this message
|
#8 |
Agreed, there are problems using the latest Intel MKL versions.
Indeed the below arch.make works for:
- 2017.7.065
- 2018.0.033
- 2018.1.038
While it does not work for:
- 2018.2.046
- 2018.3.051
I have filed a bug-report @ Intel MKL forum, and we'll have to see their response.
SIESTA_
FC=mpiifort
FFLAGS = -O2 -xHost -fp-model precise -prec-sqrt -prec-div \
-fimf-
-double-size 64 -real-size 32 \
-warn unused,
FFLAGS_SPECIAL= -O1 -xHost -ip -mp1 -fpp -heap-arrays 1024 -i4 \
-double-size 64 -real-size 32 -fp-model precise \
-warn unused,
DUMMY_FOX=
FFLAGS_DEBUG=-g -O0 -debug full -traceback -C
LDFLAGS= -static-intel -static-libgcc
RANLIB=ranlib
FC_SERIAL=ifort
#
NETCDF_LIBS=
NETCDF_INTERFACE=
FPPFLAGS_CDF=
MPI_INTERFACE=
MKL_INCLUDE=
MPI_LIBS=
MKL_LIBS=
MPI_INCLUDE=
INCFLAGS=
#
FPPFLAGS_MPI=-DMPI -DMPI_TIMING -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DSIESTA__NO_MRRR
##
NETCDF_LIBS=
NETCDF_INTERFACE=
##
LIBS= $(MPI_LIB) -mkl=parallel \
${MKLROOT}
${MKLROOT}
-Wl,--start-group \
${MKLROOT}
${MKLROOT}
${MKLROOT}
${MKLROOT}
-Wl,--end-group -lstdc++ -lpthread -lm -ldl
#
SYS=nag
FPPFLAGS= $(FPPFLAGS_CDF) $(FPPFLAGS_MPI)
##
atom.o: atom.F
$(FC) -c $(FFLAGS_SPECIAL) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
state_analysis.o: state_analysis.F
$(FC) -c $(FFLAGS_SPECIAL) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
.F.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $<
.f.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $<
.F90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $<
.f90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $<
Can you help with this problem?
Provide an answer of your own, or ask Franco Moitzi for more information if necessary.
