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

This commit is contained in:
Axel Kohlmeyer 2018-11-03 00:21:10 -04:00
parent ac11d66d5a
commit badfdd7433
3 changed files with 47 additions and 50 deletions
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44
examples/USER/plumed/log.24Oct18.peptide-plumed.g++.4
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@ -15,7 +15,7 @@ kspace_style pppm 0.0001
read_data data.peptide read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) 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 ... reading atoms ...
2004 atoms 2004 atoms
reading velocities ... reading velocities ...
@ -85,7 +85,7 @@ PPPM initialization ...
estimated absolute RMS force accuracy = 0.0228209 estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05 estimated relative force accuracy = 6.87243e-05
using double precision FFTs using double precision FFTs
3d grid and FFT values/proc = 6776 1800 3d grid and FFT values/proc = 4312 960
Neighbor list info ... Neighbor list info ...
update every 1 steps, delay 5 steps, check yes update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
@ -107,7 +107,7 @@ SHAKE stats (type/ave/delta) on step 0
14 0.96 0 14 0.96 0
18 0.957206 4.37979e-05 18 0.957206 4.37979e-05
31 104.519 0.00396029 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 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 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 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 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 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 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 SHAKE stats (type/ave/delta) on step 100
4 1.111 2.06868e-06 4 1.111 2.06868e-06
6 0.996999 2.09521e-06 6 0.996999 2.09521e-06
@ -128,31 +128,31 @@ SHAKE stats (type/ave/delta) on step 100
14 0.959999 0 14 0.959999 0
18 0.9572 9.14098e-06 18 0.9572 9.14098e-06
31 104.52 0.000760401 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 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 Performance: 14.947 ns/day, 1.606 hours/ns, 86.497 timesteps/s
99.5% CPU use with 2 MPI tasks x 1 OpenMP threads 97.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.97985 | 0.98197 | 0.98409 | 0.2 | 79.75 Pair | 0.84633 | 0.86651 | 0.88617 | 1.6 | 74.21
Bond | 0.0033333 | 0.0035326 | 0.003732 | 0.3 | 0.29 Bond | 0.0010614 | 0.0027132 | 0.004288 | 3.0 | 0.23
Kspace | 0.096567 | 0.098457 | 0.10035 | 0.6 | 8.00 Kspace | 0.095008 | 0.1162 | 0.13491 | 4.3 | 9.95
Neigh | 0.088877 | 0.088888 | 0.088898 | 0.0 | 7.22 Neigh | 0.07834 | 0.078424 | 0.078516 | 0.0 | 6.72
Comm | 0.018255 | 0.018347 | 0.01844 | 0.1 | 1.49 Comm | 0.03314 | 0.033299 | 0.033426 | 0.1 | 2.85
Output | 0.00024843 | 0.00031161 | 0.00037479 | 0.0 | 0.03 Output | 0.00036979 | 0.00076199 | 0.0019338 | 0.0 | 0.07
Modify | 0.037596 | 0.037645 | 0.037695 | 0.0 | 3.06 Modify | 0.063471 | 0.064011 | 0.065312 | 0.3 | 5.48
Other | | 0.00222 | | | 0.18 Other | | 0.005751 | | | 0.49
Nlocal: 1002 ave 1010 max 994 min Nlocal: 501 ave 512 max 492 min
Histogram: 1 0 0 0 0 0 0 0 0 1 Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 8639.5 ave 8651 max 8628 min Nghost: 6570.25 ave 6604 max 6529 min
Histogram: 1 0 0 0 0 0 0 0 0 1 Histogram: 1 0 0 1 0 0 0 0 1 1
Neighs: 353980 ave 355907 max 352054 min Neighs: 176990 ave 181122 max 173551 min
Histogram: 1 0 0 0 0 0 0 0 0 1 Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 707961 Total # of neighbors = 707961
Ave neighs/atom = 353.274 Ave neighs/atom = 353.274

33
lib/plumed/Install.py
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@ -35,10 +35,16 @@ version = "2.4.3"
# known checksums for different PLUMED versions. used to validate the download. # known checksums for different PLUMED versions. used to validate the download.
checksums = { \ checksums = { \
'2.4.2' : '0f66f24b4c763ae8b2f39574113e9935', \ '2.4.2' : '88188743a6e03ef076e5377d03ebb0e7', \
'2.4.3' : 'dc38de0ffd59d13950d8f1ef1ce05574', \ '2.4.3' : 'b1be7c48971627febc11c61b70767fc5', \
'2.5b' : 'e341bdef469be1da058b8a0b97a3db22', \
} }
#checksums = { \
# '2.4.2' : '0f66f24b4c763ae8b2f39574113e9935', \
# '2.4.3' : 'dc38de0ffd59d13950d8f1ef1ce05574', \
# }
# print error message or help # print error message or help
def error(str=None): def error(str=None):
if not str: print(help) if not str: print(help)
@ -146,8 +152,10 @@ if (not buildflag and not pathflag):
# download and unpack plumed2 tarball # download and unpack plumed2 tarball
if buildflag: if buildflag:
url = "https://github.com/plumed/plumed2/archive/v%s.tar.gz" % version url = "https://github.com/plumed/plumed2/releases/download/v%s/plumed-src-%s.tgz" % (version,version)
filename = "v%s.tar.gz" %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 ...") print("Downloading plumed ...")
geturl(url,filename) geturl(url,filename)
@ -156,22 +164,26 @@ if buildflag:
if not checkmd5sum(checksums[version],filename): if not checkmd5sum(checksums[version],filename):
error("Checksum for plumed2 library does not match") error("Checksum for plumed2 library does not match")
print("Unpacking plumed2 tarball ...") print("Unpacking plumed2 source tarball ...")
if os.path.exists("%s/plumed2-%s" % (homepath,version)): if os.path.exists("%s/plumed-%s" % (homepath,version)):
cmd = 'rm -rf "%s/plumed2-%s"' % (homepath,version) cmd = 'rm -rf "%s/plumed-%s"' % (homepath,version)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) 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)): if os.path.exists("%s/plumed2" % (homepath)):
cmd = 'rm -rf "%s/plumed2"' % (homepath) cmd = 'rm -rf "%s/plumed2"' % (homepath)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) 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) 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 # build plumed
if buildflag: if buildflag:
print("Building plumed ...") 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) txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
print(txt.decode('UTF-8')) print(txt.decode('UTF-8'))
# #
@ -190,4 +202,5 @@ if linkflag:
if os.path.isfile("Makefile.lammps.static"): if os.path.isfile("Makefile.lammps.static"):
print("Creating Makefile.lammps") print("Creating Makefile.lammps")
cmd = 'cat liblink/plumed/src/lib/Plumed.inc.static Makefile.lammps.static > 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)

20
src/USER-PLUMED/fix_plumed.cpp
View File

@ -34,25 +34,9 @@
#include "pair.h" #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 #define __PLUMED_WRAPPER_CXX 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
#include "plumed/wrapper/Plumed.h" #include "plumed/wrapper/Plumed.h"