So the mdrun-502-902-avx-64.exe program is tying up 4 cores but it is only using one core (about 27%). However, if I use 1 core (refreshing the GPUGrid account on BOINC Manager telling it to use 1 core) it uses the same amount of cpu (27% according to task manager) but the time estimate quadruples and the progress is markedly slower. I don't get it. Its obvious that it isn't using 4 cores when it is supposed to... I would expect AVX running on 4 cores would be moderately warm or hot running. Even process explorer reports only about 26 to 27% cpu usage.

Install Process Explorer. Find the process that is running the task. Double click it. Click the Threads tab. Sort that Threads tab by CPU descending.

If it's running 4-threaded, then the Threads tab should show 4 threads utilizing some CPU.

What do you see there?

Install Process Explorer. Find the process that is running the task. Double click it. Click the Threads tab. Sort that Threads tab by CPU descending.

If it's running 4-threaded, then the Threads tab should show 4 threads utilizing some CPU.

What do you see there?

mdrun-502-902-avx-64.exe properties

3 Threads.

Thread 1 is 4664 using 24% cpu called mdrun-502-902-avx-64.exe!bwlzh_decompress_verbose+0x131ac

Thread 2 is 4432 using < 0.01% cpu called mdrun-502-902-avx-64.exe!bwlzh_decompress_verbose+0x12880

Thread 3 is 2124 called MSVCR100.dll!endthreadex+0x60

Looks buggered. Would you kill it and start it again?

MAtt

Sorry I literally killed the process without thinking about it. However, I did download another one and it is doing the exact same thing (using 3 threads, 24.8% cpu). The thread IDs have changed but they are still using the same start addresses:

mdrun-502-902-avx-64.exe!bwlzh_decompress_verbose+0x131ac

mdrun-502-902-avx-64.exe!bwlzh_decompress_verbose+0x12880

MSVCR100.dll!endthreadex+0x60

Yes estimates are incorrect.
With AVX 8 threads- the task will take a total ~16hr.

I've been though this thread. I installed BOINC 7.4.22 and the estimated remaining time dropped dramatically.

I also Googled AVX. I guess my AMD FX 8350 has it, but do I need to do anything to activate it?

How many hours for AVX 4 threads? In 24 hours I only did 20%.

I also Googled AVX. I guess my AMD FX 8350 has it, but do I need to do anything to activate it?

According to the AMD website, FX processors do have the AVX instruction set. All you need then is a compatible operating system. Windows 7 SP1 and Windows 8/8.1 do use and recognize the AVX instruction set so you should be set.

After resetting the project, same thing happened. It says "using 8 threads", yet it only uses one (13% CPU usage).
The progres.txt file doesn't update at all after this:

Log file opened on Fri Oct 24 16:28:33 2014
Host: unknown pid: 5364 rank ID: 0 number of ranks: 1
GROMACS: mdrun-502-902-avx-64, VERSION 5.0.2

GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
Gerrit Groenhof Christoph Junghans Peter Kasson Carsten Kutzner
Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
Peter Tieleman Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2014, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS: mdrun-502-902-avx-64, VERSION 5.0.2
Executable: D:\ProgramData\BOINC\slots\0\projects\www.gpugrid.net\mdrun-502-902-avx-64.exe
Library dir: C:\Program Files\Gromacs\share\gromacs\top
Command line:
mdrun-502-902-avx-64 -ntomp 8 -nt 8 -x traj.xtc -s topol.tpr -g progress.log -cpi state.cpt

Gromacs version: VERSION 5.0.2
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled
GPU support: disabled
invsqrt routine: gmx_software_invsqrt(x)
SIMD instructions: AVX_256
FFT library: fftw3
RDTSCP usage: enabled
C++11 compilation: disabled
TNG support: enabled
Tracing support: disabled
Built on: Unknown date
Built by: Anonymous@unknown [CMAKE]
Build OS/arch: Windows-6.1 AMD64
Build CPU vendor: GenuineIntel
Build CPU brand: Intel(R) Core(TM) i3-2365M CPU @ 1.40GHz
Build CPU family: 6 Model: 42 Stepping: 7
Build CPU features: apic clfsh cmov cx8 lahf_lm mmx msr pse rdtscp sse2 sse3 ssse3
C compiler: C:/Program Files (x86)/Microsoft Visual Studio 10.0/VC/bin/x86_amd64/cl.exe MSVC 16.0.30319.1
C compiler flags: /arch:AVX /DWIN32 /D_WINDOWS /W3 /MD /O2 /Ob2 /D NDEBUG
C++ compiler: C:/Program Files (x86)/Microsoft Visual Studio 10.0/VC/bin/x86_amd64/cl.exe MSVC 16.0.30319.1
C++ compiler flags: /arch:AVX /DWIN32 /D_WINDOWS /W3 /GR /EHsc /wd4800 /wd4355 /wd4996 /wd4305 /wd4244 /wd4101 /wd4267 /wd4090 /MD /O2 /Ob2 /D NDEBUG
Boost version: 1.55.0 (internal)



++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-------- -------- --- Thank You --- -------- --------

Changing nstlist from 10 to 20, rlist from 0.9 to 0.928

Input Parameters:
integrator = md-vv
tinit = 0
dt = 0.002
nsteps = 5000000
init-step = 0
simulation-part = 1
comm-mode = Linear
nstcomm = 100
bd-fric = 0
ld-seed = 1993
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstcalcenergy = 100
nstenergy = 1000
nstxout-compressed = 25000
compressed-x-precision = 1000
cutoff-scheme = Verlet
nstlist = 20
ns-type = Grid
pbc = xyz
periodic-molecules = FALSE
verlet-buffer-tolerance = 0.005
rlist = 0.928
rlistlong = 0.928
nstcalclr = 10
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 0.9
epsilon-r = 1
epsilon-rf = inf
vdw-type = Cut-off
vdw-modifier = Potential-switch
rvdw-switch = 0.75
rvdw = 0.9
DispCorr = No
table-extension = 1
fourierspacing = 0.1
fourier-nx = 64
fourier-ny = 64
fourier-nz = 64
pme-order = 4
ewald-rtol = 1e-005
ewald-rtol-lj = 1e-005
lj-pme-comb-rule = Geometric
ewald-geometry = 0
epsilon-surface = 0
implicit-solvent = No
gb-algorithm = Still
nstgbradii = 1
rgbradii = 1
gb-epsilon-solvent = 80
gb-saltconc = 0
gb-obc-alpha = 1
gb-obc-beta = 0.8
gb-obc-gamma = 4.85
gb-dielectric-offset = 0.009
sa-algorithm = Ace-approximation
sa-surface-tension = 2.05016
tcoupl = Nose-Hoover
nsttcouple = 10
nh-chain-length = 10
print-nose-hoover-chain-variables = FALSE
pcoupl = No
pcoupltype = Isotropic
nstpcouple = -1
tau-p = 1
compressibility (3x3):
compressibility[ 0]={0.00000e+000, 0.00000e+000, 0.00000e+000}
compressibility[ 1]={0.00000e+000, 0.00000e+000, 0.00000e+000}
compressibility[ 2]={0.00000e+000, 0.00000e+000, 0.00000e+000}
ref-p (3x3):
ref-p[ 0]={0.00000e+000, 0.00000e+000, 0.00000e+000}
ref-p[ 1]={0.00000e+000, 0.00000e+000, 0.00000e+000}
ref-p[ 2]={0.00000e+000, 0.00000e+000, 0.00000e+000}
refcoord-scaling = No
posres-com (3):
posres-com[0]=0.00000e+000
posres-com[1]=0.00000e+000
posres-com[2]=0.00000e+000
posres-comB (3):
posres-comB[0]=0.00000e+000
posres-comB[1]=0.00000e+000
posres-comB[2]=0.00000e+000
QMMM = FALSE
QMconstraints = 0
QMMMscheme = 0
MMChargeScaleFactor = 1
qm-opts:
ngQM = 0
constraint-algorithm = Shake
continuation = FALSE
Shake-SOR = FALSE
shake-tol = 0.0001
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
nwall = 0
wall-type = 9-3
wall-r-linpot = -1
wall-atomtype[0] = -1
wall-atomtype[1] = -1
wall-density[0] = 0
wall-density[1] = 0
wall-ewald-zfac = 3
pull = no
rotation = FALSE
interactiveMD = FALSE
disre = No
disre-weighting = Conservative
disre-mixed = FALSE
dr-fc = 1000
dr-tau = 0
nstdisreout = 100
orire-fc = 0
orire-tau = 0
nstorireout = 100
free-energy = no
cos-acceleration = 0
deform (3x3):
deform[ 0]={0.00000e+000, 0.00000e+000, 0.00000e+000}
deform[ 1]={0.00000e+000, 0.00000e+000, 0.00000e+000}
deform[ 2]={0.00000e+000, 0.00000e+000, 0.00000e+000}
simulated-tempering = FALSE
E-x:
n = 0
E-xt:
n = 0
E-y:
n = 0
E-yt:
n = 0
E-z:
n = 0
E-zt:
n = 0
swapcoords = no
adress = FALSE
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 48414
ref-t: 300
tau-t: 0.8
annealing: No
annealing-npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp-flags[ 0]: 0

And the stderr.txt gives this:

BOINC wrapper for GROMACS.
Arg 0 [projects/www.gpugrid.net/mdrun-502-902-avx-64.exe]
Arg 1 [--nthreads]
Arg 2 [8]
BOINC running with [8] threads
BOINC resolving [traj.xtc] to [traj.xtc]
BOINC resolving [topol.tpr] to [topol.tpr]
BOINC resolving [progress.log] to [progress.log]
BOINC resolving [state.cpt] to [state.cpt]
GROMACS: mdrun-502-902-avx-64, VERSION 5.0.2

GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
Gerrit Groenhof Christoph Junghans Peter Kasson Carsten Kutzner
Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
Peter Tieleman Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2014, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS: mdrun-502-902-avx-64, VERSION 5.0.2
Executable: D:\ProgramData\BOINC\slots\0\projects\www.gpugrid.net\mdrun-502-902-avx-64.exe
Library dir: C:\Program Files\Gromacs\share\gromacs\top
Command line:
mdrun-502-902-avx-64 -ntomp 8 -nt 8 -x traj.xtc -s topol.tpr -g progress.log -cpi state.cpt

Reading file topol.tpr, VERSION 4.6.1 (single precision)
Note: file tpx version 83, software tpx version 100
Changing nstlist from 10 to 20, rlist from 0.9 to 0.928

So... apparently it gets stuck running on 1 thread doing apparently nothing at all.

---

After resetting the project, same thing happened. It says "using 8 threads", yet it only uses one (13% CPU usage).
The progres.txt file doesn't update at all after this:

Excellent point... I couldn't remember how often the progress.log file updates after the program starts. Like workunits do for some other projects, I figured it has some preliminary work to do before started really crunching with all threads. I thought it was a problem with my computer. It doesn't seem like the program is spinning up enough threads.

And reviewing the older MT tasks I've crunched there is usually a note in stderr.txt or progress.log that mentions running 1 MPI thread and 4 OpenMP threads. I don't see the same note using the AVX program. Perhaps its something very simple like a missing command line argument?

Yes estimates are incorrect.
With AVX 8 threads- the task will take a total ~16hr.

I've been though this thread. I installed BOINC 7.4.22 and the estimated remaining time dropped dramatically.

I also Googled AVX. I guess my AMD FX 8350 has it, but do I need to do anything to activate it?

How many hours for AVX 4 threads? In 24 hours I only did 20%.

Note: These estimates are for Intel AVX. I'm unsure about AMD AVX CPUMD times.
AMD AVX instructions are computed differently than Intel's. AMD has more Integer execution ports than Floating Point.
FX modules share a AVX FP unit with threads- for every two integer core there is one 128bit AVX capable FP unit. To complete a 256bit AVX instruction: a second 128bit cycle is required. Whereas Intel Sandy/Ivy/Haswell has a 256bit AVX FP unit.

http://www.anandtech.com/show/5831/amd-trinity-review-a10-4600m-a-new-hope
http://www.anandtech.com/show/4955/the-bulldozer-review-amd-fx8150-tested/2
http://www.anandtech.com/show/6355/intels-haswell-architecture/8[/url]

After resetting the project, same thing happened. It says "using 8 threads", yet it only uses one (13% CPU usage).
The progres.txt file doesn't update at all after this:

Excellent point... I couldn't remember how often the progress.log file updates after the program starts. Like workunits do for some other projects, I figured it has some preliminary work to do before started really crunching with all threads. I thought it was a problem with my computer. It doesn't seem like the program is spinning up enough threads.

And reviewing the older MT tasks I've crunched there is usually a note in stderr.txt or progress.log that mentions running 1 MPI thread and 4 OpenMP threads. I don't see the same note using the AVX program. Perhaps its something very simple like a missing command line argument?

The SSE2 WUs that I ran on this exact same machine updated its progress.txt showing the step number it was on every 10 seconds or so. This one though, seems to get stuck, so I'm pretty sure it's some kind of bug. The stderr.txt file does show that the WU is asking for 8 cores, yet it only "uses" 1, so it seems the bug is located after the initialization of the WU.

---

Are CPUMD SSE2/4 tasks being sent to AVX hosts?

Are CPUMD SSE2/4 tasks being sent to AVX hosts?

I do not believe so. I have requested a few CPU test apps (over the past couple of days) and have always gotten the AVX ones. I suppose I could downgrade the BOINC client so it stops recognizing AVX, or set up a specific app_info.xml file, but I wouldn't have any idea what to put in it.

I keep getting CPU WUs (that don't work...) even though I unchecked the "Use CPU?" in the setting page for GPUGRID (along with unchecking everything BUT ACEMD LONG RUNS). If the AVX WU problem is not fixed or the whole not-obeying the settings thing, then I'm going to be forced to detach the project entirely (I don't want to play cop and manually abort the CPU WUs that are bugged, it defeats the whole set-it-and-forget-it purpose of BOINC...).

---

does it work for pricese puppy 5.7? I do not get any WUs. Thanks.

Who is Princess Puppy?

I think Puppy Linux Precise 5.7.1
http://www.puppylinux.com/ and http://bkhome.org/blog2/?viewDetailed=00346 for precise

:D

Does anybody else have unusually high Task duration correction for GPUGRID since computing or downloading a MDCPU task?

Since I've completed or downloaded a CPUMD task-- GPUGRID Task duration correction factor (9.829525) has sky rocketed. Other Projects are have the correct factor number and task estimates are within normal ranges for CPU/GPU completion times.
Currently there is no CPUMD tasks running or in cache while factor has stayed the same. I just downloaded a new GPU task and the estimate time is at 370Hr.(All CPU/GPU task from GPUGRID are abnormal estimates for a week or so) 7.4.21 Client reverting task factor to the proper number isn't happening (re-setting/letting all tasks in cache finish/completing 10 GPU tasks since)
What is causing the continuation of high correction factors?

Also- Will future MD tasks have GPU support enabled?

Also- Will MD task in future have GPU support enabled?

Not in the short-to-medium term - the point of this application is to use CPU.
In the long term, it might support AMD GPUs, but don't quote me on that.

Matt

The buggy Windows AVX app is gone now. Please abort any instances of it still running. It's replaced with the working SSE2 app.

I am running the CPU application version 9.01 I noticed when I opened the progress text file it tells me I am running the following CPU

Build CPU brand:    Intel(R) Core(TM) i3-2365M CPU @ 1.40GHz

however I am actually running and I 7 980 X the task is currently 62.9% complete. With another estimated 16 hours to go task name 1981-MJHARVEY_CPUDHFR-0-1-RND0908_2

Has anyone else noticed this? The reporting of wrong CPU.
Also could somebody please explain to me how the time is worked out in the progress file? E.g. after 3686000 steps it says under time 7372.00000

The buggy Windows AVX app is gone now. Please abort any instances of it still running. It's replaced with the working SSE2 app.

Working? Yes, but it stops one of my two GPU tasks:



I gave BOINC another CPU thread to play with and the waiting-to-run task restarted, but I immediately got another MJHARVEY, which is hardly likely to complete before its deadline...