Skip to content
Snippets Groups Projects
Commit badfdd74 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

download only the plumed-src package and include further tweaks to be compatible with plumed 2.5b

parent ac11d66d
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
examples/USER/plumed/log.24Oct18.peptide-plumed.g++.4
+ 23
− 23
View file @ badfdd74
......@@ -15,7 +15,7 @@ kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 2 MPI processor grid
1 by 2 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
......@@ -85,7 +85,7 @@ PPPM initialization ...
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
3d grid and FFT values/proc = 4312 960
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
......@@ -107,7 +107,7 @@ SHAKE stats (type/ave/delta) on step 0
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Per MPI rank memory allocation (min/avg/max) = 16.81 | 16.82 | 16.83 Mbytes
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 0
10 276.9783 -5234.3057 -6348.6171 1114.3114 -6421.6171 17.024361 0.47785504
......@@ -118,7 +118,7 @@ Step Temp TotEng PotEng KinEng E_pair E_bond f_2
60 273.01449 -5217.7381 -6316.1026 1098.3646 -6406.4709 21.800931 0.92327815
70 274.67549 -5221.0246 -6326.0716 1105.047 -6409.7721 19.41235 0.0016975896
80 273.74824 -5224.7613 -6326.0778 1101.3165 -6418.5055 19.206793 0.48550348
90 284.32594 -5229.195 -6373.0667 1143.8717 -6461.3467 21.124789 0.5468014
90 284.32594 -5229.195 -6373.0667 1143.8717 -6461.3466 21.124789 0.5468014
SHAKE stats (type/ave/delta) on step 100
4 1.111 2.06868e-06
6 0.996999 2.09521e-06
......@@ -128,31 +128,31 @@ SHAKE stats (type/ave/delta) on step 100
14 0.959999 0
18 0.9572 9.14098e-06
31 104.52 0.000760401
100 270.40648 -5234.9604 -6322.8327 1087.8723 -6417.73 19.666404 0.0094784372
100 270.40648 -5234.9604 -6322.8327 1087.8723 -6417.73 19.666404 0.009478437
101 270.99811 -5235.8295 -6326.082 1090.2525 -6418.8974 17.285816 0.086681332
Loop time of 1.23137 on 2 procs for 101 steps with 2004 atoms
Loop time of 1.16767 on 4 procs for 101 steps with 2004 atoms
Performance: 14.173 ns/day, 1.693 hours/ns, 82.022 timesteps/s
99.5% CPU use with 2 MPI tasks x 1 OpenMP threads
Performance: 14.947 ns/day, 1.606 hours/ns, 86.497 timesteps/s
97.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.97985 | 0.98197 | 0.98409 | 0.2 | 79.75
Bond | 0.0033333 | 0.0035326 | 0.003732 | 0.3 | 0.29
Kspace | 0.096567 | 0.098457 | 0.10035 | 0.6 | 8.00
Neigh | 0.088877 | 0.088888 | 0.088898 | 0.0 | 7.22
Comm | 0.018255 | 0.018347 | 0.01844 | 0.1 | 1.49
Output | 0.00024843 | 0.00031161 | 0.00037479 | 0.0 | 0.03
Modify | 0.037596 | 0.037645 | 0.037695 | 0.0 | 3.06
Other | | 0.00222 | | | 0.18
Nlocal: 1002 ave 1010 max 994 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8639.5 ave 8651 max 8628 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 353980 ave 355907 max 352054 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Pair | 0.84633 | 0.86651 | 0.88617 | 1.6 | 74.21
Bond | 0.0010614 | 0.0027132 | 0.004288 | 3.0 | 0.23
Kspace | 0.095008 | 0.1162 | 0.13491 | 4.3 | 9.95
Neigh | 0.07834 | 0.078424 | 0.078516 | 0.0 | 6.72
Comm | 0.03314 | 0.033299 | 0.033426 | 0.1 | 2.85
Output | 0.00036979 | 0.00076199 | 0.0019338 | 0.0 | 0.07
Modify | 0.063471 | 0.064011 | 0.065312 | 0.3 | 5.48
Other | | 0.005751 | | | 0.49
Nlocal: 501 ave 512 max 492 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 6570.25 ave 6604 max 6529 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Neighs: 176990 ave 181122 max 173551 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 707961
Ave neighs/atom = 353.274
......
lib/plumed/Install.py
+ 23
− 10
View file @ badfdd74
......@@ -35,10 +35,16 @@ version = "2.4.3"
# known checksums for different PLUMED versions. used to validate the download.
checksums = { \
'2.4.2' : '0f66f24b4c763ae8b2f39574113e9935', \
'2.4.3' : 'dc38de0ffd59d13950d8f1ef1ce05574', \
'2.4.2' : '88188743a6e03ef076e5377d03ebb0e7', \
'2.4.3' : 'b1be7c48971627febc11c61b70767fc5', \
'2.5b' : 'e341bdef469be1da058b8a0b97a3db22', \
}
#checksums = { \
# '2.4.2' : '0f66f24b4c763ae8b2f39574113e9935', \
# '2.4.3' : 'dc38de0ffd59d13950d8f1ef1ce05574', \
# }
# print error message or help
def error(str=None):
if not str: print(help)
......@@ -146,8 +152,10 @@ if (not buildflag and not pathflag):
# download and unpack plumed2 tarball
if buildflag:
url = "https://github.com/plumed/plumed2/archive/v%s.tar.gz" % version
filename = "v%s.tar.gz" %version
url = "https://github.com/plumed/plumed2/releases/download/v%s/plumed-src-%s.tgz" % (version,version)
filename = "plumed-src-%s.tar.gz" %version
#url = "https://github.com/plumed/plumed2/archive/v%s.tar.gz" % version
#filename = "v%s.tar.gz" %version
print("Downloading plumed ...")
geturl(url,filename)
......@@ -156,22 +164,26 @@ if buildflag:
if not checkmd5sum(checksums[version],filename):
error("Checksum for plumed2 library does not match")
print("Unpacking plumed2 tarball ...")
if os.path.exists("%s/plumed2-%s" % (homepath,version)):
cmd = 'rm -rf "%s/plumed2-%s"' % (homepath,version)
print("Unpacking plumed2 source tarball ...")
if os.path.exists("%s/plumed-%s" % (homepath,version)):
cmd = 'rm -rf "%s/plumed-%s"' % (homepath,version)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
#if os.path.exists("%s/plumed2-%s" % (homepath,version)):
# cmd = 'rm -rf "%s/plumed2-%s"' % (homepath,version)
# subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
if os.path.exists("%s/plumed2" % (homepath)):
cmd = 'rm -rf "%s/plumed2"' % (homepath)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
cmd = 'cd "%s"; tar -xzvf v%s.tar.gz' % (homepath,version)
cmd = 'cd "%s"; tar -xzvf %s' % (homepath,filename)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
os.remove("%s/v%s.tar.gz" % (homepath,version))
os.remove("%s/%s" % (homepath,filename))
# build plumed
if buildflag:
print("Building plumed ...")
cmd = 'cd %s/plumed2-%s; ./configure --prefix=%s/plumed2 ; make ; make install' % (homepath,version,homepath)
cmd = 'cd %s/plumed-%s; ./configure --prefix=%s/plumed2 --enable-static-patch ; make ; make install' % (homepath,version,homepath)
#cmd = 'cd %s/plumed2-%s; ./configure --prefix=%s/plumed2 --enable-static-patch ; make ; make install' % (homepath,version,homepath)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
print(txt.decode('UTF-8'))
#
......@@ -190,4 +202,5 @@ if linkflag:
if os.path.isfile("Makefile.lammps.static"):
print("Creating Makefile.lammps")
cmd = 'cat liblink/plumed/src/lib/Plumed.inc.static Makefile.lammps.static > Makefile.lammps'
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
src/USER-PLUMED/fix_plumed.cpp
+ 2
− 18
View file @ badfdd74
......@@ -34,25 +34,9 @@
#include "pair.h"
/*
Do not link plumed directly but rather do it at runtime
Use statically linked C++ interface to plumed
*/
#define __PLUMED_WRAPPER_LINK_RUNTIME 1
/*
Make sure the inline C++ interface is not included here.
Should not be necessary, but it doesn't hurt.
*/
#define __PLUMED_WRAPPER_CXX 0
/*
Tell Plumed.h to emit the whole implementation
*/
#define __PLUMED_WRAPPER_IMPLEMENTATION 1
/*
Emit fortran wrappers
*/
#define __PLUMED_WRAPPER_FORTRAN 1
#define __PLUMED_WRAPPER_CXX 1
#include "plumed/wrapper/Plumed.h"
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment