Closed e-kwsm closed 4 years ago
Hi,
There should not be any problem there. Can you provide us your input files, the command line you used and your execution setup.
Thanks
Thanks @lhjolly for quick reply.
I built Tinker-HP with the follows configuration:
diff --git a/v1.1/2decomp_fft/src/Makefile.inc b/v1.1/2decomp_fft/src/Makefile.inc
index c03d26eede12..bb6d05f40c57 100644
--- a/v1.1/2decomp_fft/src/Makefile.inc
+++ b/v1.1/2decomp_fft/src/Makefile.inc
@@ -37 +37 @@ else ifeq ($(FFT),fftw3_f03)
- FFTW_PATH=/usr/local/fftw-3.3.4/
+ FFTW_PATH=/path/to/fftw/3.3.8
@@ -55 +55 @@ endif
-F90=mpif90
+F90=mpiifort
@@ -60 +60 @@ CPPFLAGS=-cpp
-CRAYPTR=-fcray-pointer
+CRAYPTR=#-fcray-pointer
diff --git a/v1.1/source/Makefile b/v1.1/source/Makefile
index 5e0924696e7d..e0c168c792a4 100644
--- a/v1.1/source/Makefile
+++ b/v1.1/source/Makefile
@@ -4 +4 @@
-RunF77 = mpif90
+RunF77 = mpiifort
@@ -9 +9 @@ FFTDECOMP = -I$(FFTDECOMPDIR)/include -L$(FFTDECOMPDIR)/lib -l2decomp_fft
-BLAS = -I$(MKLDIR)/include -L$(MKLDIR)/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread #-lm
+BLAS = -mkl
@@ -14 +14 @@ BLAS = -I$(MKLDIR)/include -L$(MKLDIR)/lib/intel64 -lmkl_intel_lp64 -lmkl_int
-FFLAGS = -O3 -fopenmp -ffast-math
+FFLAGS = -O3 -qopenmp
Then
$ cd v1.1/examples
$ ./dhfr.run
######################################################################
##########################################################################
### ###
### Tinker-HP --- Software Tools for Molecular Design ###
## ##
## Version 1.1 June 2018 ##
## ##
## Copyright (c) Washington University in Saint Louis (WU) ##
## The University of Texas at Austin ##
## Sorbonne Universites, UPMC (Sorbonne) ##
## 1990-2018 ##
### All Rights Reserved ###
### ###
##########################################################################
######################################################################
License Number : PUBLIC_LICENSE
Cite this work as :
Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale
Simulations of Large Complex Systems with Advanced Polarizable Force Fields.
Louis Lagardere, Luc-Henri Jolly, Filippo Lipparini, Felix Aviat,
Benjamin Stamm, Zhifeng F. Jing, Matthew Harger, Hedieh Torabifard,
G. Andres Cisneros, Michael J. Schnieders, Nohad Gresh, Yvon Maday,
Pengyu Y. Ren, Jay W. Ponder and Jean-Philip Piquemal,
Chem. Sci., 2018, 9, 956-972 doi: 10.1039/c7sc04531j
3D Domain Decomposition
Nx = 2 Ny = 2 Nz = 2
In auto-tuning mode......
factors: 1 2 4 8
processor grid 1 by 8 time= 9.121298789978027E-004
processor grid 2 by 4 time= 3.706514835357666E-004
processor grid 4 by 2 time= 3.453195095062256E-004
processor grid 8 by 1 time= 2.660751342773438E-004
the best processor grid is probably 8 by 1
***** Using the FFTW (F2003 interface) engine *****
Smooth Particle Mesh Ewald Parameters :
Ewald Coefficient Charge Grid Dimensions B-Spline Order
0.5446 64 64 64 5
3D Domain Decomposition
Nx = 2 Ny = 2 Nz = 2
Molecular Dynamics Trajectory via r-RESPA MTS Algorithm
Fatal error in MPI_Irecv: Invalid communicator, error stack:
MPI_Irecv(170): MPI_Irecv(buf=0x2b7b79ffcd40, count=65536, dtype=0x4c000829, src=5, tag=6, comm=0x0, request=0x2b7b704ef520) failed
MPI_Irecv(90).: Invalid communicator
Hi again,
We messed up the different versions, but it should be OK now.
Thanks, now I can run all the examples.
Thanks @lhjolly for fixing #3, but I get another error like the following:
The error comes from https://github.com/TinkerTools/Tinker-HP/blob/b1f4c8172933d1cf30cbc368b6109f5e5bb734d6/v1.1/source/newinduce_pme.f#L1434-L1436 and also https://github.com/TinkerTools/Tinker-HP/blob/b1f4c8172933d1cf30cbc368b6109f5e5bb734d6/v1.1/source/newinduce_pme.f#L1483-L1485
Again I tried replacing
comm_rec
withMPI_COMM_WORLD
but execution hanged at https://github.com/TinkerTools/Tinker-HP/blob/b1f4c8172933d1cf30cbc368b6109f5e5bb734d6/v1.1/source/newinduce_pme.f#L1488-L1493Tinker-HP: b1f4c8172933d1cf30cbc368b6109f5e5bb734d6, v1.1 MPI: Intel MPI 2018U3