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invalid
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Joined: May 31, 2011
Posts: 9
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Message 2729 - Posted 10 Jul 2011 23:51:12 UTC

ubuntu 11.04 64 bit
amd cpus run fine
intel cpus give error below at end of run and before upload
output file on web site.
loaded all of everything. glut/mesa/l??++5. ia32..ldd exec all there. and anything eles I can find listed in this and other other place on the web i could find. for the past 8 weeks. now having read/ tried/ loaded/installed, etc... would someone with just a little bit of kindness help me stop the blood comming from out of my eyes and ears and let me get some sleep. :P thanks in advance....


<core_client_version>6.10.59</core_client_version>
<![CDATA[
<stderr_txt>
Unrecognized XML in parse_init_data_file: hostid
Skipping: 88368
Skipping: /hostid
Unrecognized XML in parse_init_data_file: starting_elapsed_time
Skipping: 0.000000
Skipping: /starting_elapsed_time
Unrecognized XML in parse_init_data_file: computation_deadline
Skipping: 995104875.136000
Skipping: /computation_deadline
Unrecognized XML in GLOBAL_PREFS::parse_override: mod_time
Skipping: /mod_time
Unrecognized XML in GLOBAL_PREFS::parse_override: run_gpu_if_user_active
Skipping: 1
Skipping: /run_gpu_if_user_active
Unrecognized XML in GLOBAL_PREFS::parse_override: suspend_cpu_usage
Skipping: 0.000000
Skipping: /suspend_cpu_usage
Unrecognized XML in GLOBAL_PREFS::parse_override: max_ncpus_pct
Skipping: 100.000000
Skipping: /max_ncpus_pct
Unrecognized XML in GLOBAL_PREFS::parse_override: daily_xfer_limit_mb
Skipping: 0.000000
Skipping: /daily_xfer_limit_mb
Unrecognized XML in GLOBAL_PREFS::parse_override: daily_xfer_period_days
Skipping: 0
Skipping: /daily_xfer_period_days
Unrecognized XML in parse_init_data_file: hostid
Skipping: 88368
Skipping: /hostid
Unrecognized XML in parse_init_data_file: starting_elapsed_time
Skipping: 122.282188
Skipping: /starting_elapsed_time
Unrecognized XML in parse_init_data_file: computation_deadline
Skipping: 995104875.136000
Skipping: /computation_deadline
Unrecognized XML in GLOBAL_PREFS::parse_override: mod_time
Skipping: /mod_time
Unrecognized XML in GLOBAL_PREFS::parse_override: run_gpu_if_user_active
Skipping: 1
Skipping: /run_gpu_if_user_active
Unrecognized XML in GLOBAL_PREFS::parse_override: suspend_cpu_usage
Skipping: 0.000000
Skipping: /suspend_cpu_usage
Unrecognized XML in GLOBAL_PREFS::parse_override: max_ncpus_pct
Skipping: 100.000000
Skipping: /max_ncpus_pct
Unrecognized XML in GLOBAL_PREFS::parse_override: daily_xfer_limit_mb
Skipping: 0.000000
Skipping: /daily_xfer_limit_mb
Unrecognized XML in GLOBAL_PREFS::parse_override: daily_xfer_period_days
Skipping: 0
Skipping: /daily_xfer_period_days

</stderr_txt>
<message>
<file_xfer_error>
<file_name>wu_78596477_1306997469_54288_7_1</file_name>
<error_code>-161</error_code>
</file_xfer_error>

</message>
]]>

invalid
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Message 2730 - Posted 11 Jul 2011 12:20:48 UTC

forget it

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Message 2731 - Posted 12 Jul 2011 7:12:08 UTC - in response to Message ID 2730.

forget it


H'mmm; okay; you could run the executable yourself on your crashing machine and see if it is the app (which I doubt) or the boinc client (which I suspect).

http://boinc.gorlaeus.net/download/DownLoads/Standalone/

m.
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Message 2734 - Posted 12 Jul 2011 13:16:16 UTC

done, all there.

project does not run well on intel chips.

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Message 2736 - Posted 13 Jul 2011 9:11:57 UTC

My test on Ubuntu LTS 10.04.2 (Intel(R) Core(TM)2 Quad CPU Q8400 @ 2.66GHz) with BOINC installed from the repo works just fine...

If the application fails; there should be a segfault/coredump/error message from the application executable itself. Please send it to me by running the following commands in a terminal on the machine:

$ wget http://boinc.gorlaeus.net/download/DownLoads/Standalone/Executables/Graphics/GLUT_ClassicalDynamics_Linux.x
$ wget http://boinc.gorlaeus.net/download/DownLoads/Standalone/Examples/hexane
$ ldd ./GLUT_ClassicalDynamics_Linux.x
$ ./GLUT_ClassicalDynamics_Linux.x hexane

m.

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Message 2739 - Posted 14 Jul 2011 17:34:55 UTC - in response to Message ID 2736.

# a simple hexane molecule is being investigated.

# first define some colors
color id=0 rgb=[1.0,1.0,1.0]
color id=1 rgb=[1.0,0.0,0.0]
color id=2 rgb=[0.0,1.0,0.0]
color id=3 rgb=[0.0,0.0,1.0]
color id=4 rgb=[0.3,0.3,0.3]

# define the box
box cell=[25,25,25]

# ------------------------------------------
# the carbon chain
scale x=1.5 y=1.5 z=1.5
particle m=21894.71 q=6.0 r=1.46 p=[0.0,0.0,0.0] x=[-4.0,0.0,0.0] c=4 id=1
particle x=[-2.0,0.0,0.0]
particle x=[0.0,0.0,0.0]
particle x=[2.0,0.0,0.0]
particle x=[4.0,0.0,0.0]
particle x=[6.0,0.0,0.0]

# the bonding forces between the carbons
interaction harmonic f=1.275 r0=2.89 { 1 2 }
interaction harmonic f=1.275 r0=2.89 { 2 3 }
interaction harmonic f=1.275 r0=2.89 { 3 4 }
interaction harmonic f=1.275 r0=2.89 { 4 5 }
interaction harmonic f=1.275 r0=2.89 { 5 6 }

# the bond bending forces between the carbons
interaction bending f=0.175 deg=112.4 { 1 2 3 4 5 6}

# then the torsional force between the carbons
interaction torsional f=0.0175 n=1 deg=180.0 { 1 2 3 4 5 6}


# ------------------------------------------
# now for the hydrogen atoms on C1
translate x=-4.0
scale x=2.25 y=2.25 z=2.25
particle m=1827.81 q=1.0 r=0.701 p=[0.0,0.0,0.0] x=[1.0,0.0,0.0] c=0 id=100
particle x=[0.0,1.0,0.0]
particle x=[0.0,0.0,1.0]

# the H-C-H bending forces of the first CH3
interaction bending f=0.175 deg=107.7 { 100 1 101 }
interaction bending f=0.175 deg=107.7 { 101 1 102 }
interaction bending f=0.175 deg=107.7 { 102 1 100 }

#the H-C-C bending forces of the first CH3
interaction bending f=0.175 deg=111.2 { 2 1 100 }
interaction bending f=0.175 deg=111.2 { 2 1 101 }
interaction bending f=0.175 deg=111.2 { 2 1 102 }

# the bonding interactions of the first CH3
interaction harmonic f=1.195 r0=3.76 { 1 100 }
interaction harmonic f=1.195 r0=3.76 { 1 101 }
interaction harmonic f=1.195 r0=3.76 { 1 102 }


# ------------------------------------------
# now for the hydrogen atoms on C2
translate x=-2.0
scale x=2.25 y=2.25 z=2.25
particle x=[1.0,0.0,0.0] id=200
particle x=[0.0,1.0,0.0]

# the CH2 H-C-H bending on C2
interaction bending f=0.175 deg=106.1 { 200 2 201 }

# the four CH2 C-C-H bending on C2
interaction bending f=0.175 deg=109.5 { 1 2 200 }
interaction bending f=0.175 deg=109.5 { 1 2 201 }
interaction bending f=0.175 deg=109.5 { 3 2 200 }
interaction bending f=0.175 deg=109.5 { 3 2 201 }

# the bonding interactions of the first CH2 on C2
interaction harmonic f=1.195 r0=3.76 { 2 200 }
interaction harmonic f=1.195 r0=3.76 { 2 201 }


# ------------------------------------------
# now for the hydrogen atoms on C3
translate x=0.0
scale x=2.25 y=2.25 z=2.25
particle x=[1.0,0.0,0.0] id=300
particle x=[0.0,1.0,0.0]

# the CH2 H-C-H bending on C3
interaction bending f=0.175 deg=106.1 { 300 3 301 }

# the four CH2 C-C-H bending on C3
interaction bending f=0.175 deg=109.5 { 2 3 300 }
interaction bending f=0.175 deg=109.5 { 2 3 301 }
interaction bending f=0.175 deg=109.5 { 4 3 300 }
interaction bending f=0.175 deg=109.5 { 4 3 301 }

# the bonding interactions of the second CH2 on C3
interaction harmonic f=1.195 r0=3.76 { 3 300 }
interaction harmonic f=1.195 r0=3.76 { 3 301 }


# ------------------------------------------
# now for the hydrogen atoms on C4
translate x=2.0
scale x=2.25 y=2.25 z=2.25
particle x=[1.0,0.0,0.0] id=400
particle x=[0.0,1.0,0.0]

# the CH2 H-C-H bending on C4
interaction bending f=0.175 deg=106.1 { 400 4 401 }

# the four CH2 C-C-H bending on C4
interaction bending f=0.175 deg=109.5 { 3 4 400 }
interaction bending f=0.175 deg=109.5 { 3 4 401 }
interaction bending f=0.175 deg=109.5 { 5 4 400 }
interaction bending f=0.175 deg=109.5 { 5 4 401 }

# the bonding interactions of the second CH2 on C3
interaction harmonic f=1.195 r0=3.76 { 4 400 }
interaction harmonic f=1.195 r0=3.76 { 4 401 }


# ------------------------------------------
# now for the hydrogen atoms on C5
translate x=4.0
scale x=2.25 y=2.25 z=2.25
particle x=[1.0,0.0,0.0] id=500
particle x=[0.0,1.0,0.0]

# the CH2 H-C-H bending on C5
interaction bending f=0.175 deg=106.1 { 500 5 501 }

# the four CH2 C-C-H bending on C5
interaction bending f=0.175 deg=109.5 { 4 5 500 }
interaction bending f=0.175 deg=109.5 { 4 5 501 }
interaction bending f=0.175 deg=109.5 { 6 5 500 }
interaction bending f=0.175 deg=109.5 { 6 5 501 }

# the bonding interactions of the second CH2 on C5
interaction harmonic f=1.195 r0=3.76 { 5 500 }
interaction harmonic f=1.195 r0=3.76 { 5 501 }


# ------------------------------------------
# now for the hydrogen atoms on C6
translate x=6.0
scale x=2.25 y=2.25 z=2.25
particle x=[1.0,0.0,0.0] id=600
particle x=[0.0,1.0,0.0]
particle x=[0.0,0.0,1.0]

# the H-C-H bending forces of the second CH3
interaction bending f=0.175 deg=107.7 { 600 6 601 }
interaction bending f=0.175 deg=107.7 { 601 6 602 }
interaction bending f=0.175 deg=107.7 { 602 6 600 }

#the H-C-C bending forces of the second CH3
interaction bending f=0.175 deg=111.2 { 5 6 600 }
interaction bending f=0.175 deg=111.2 { 5 6 601 }
interaction bending f=0.175 deg=111.2 { 5 6 602 }

# the bonding interactions of the first CH3
interaction harmonic f=1.195 r0=3.76 { 6 600 }
interaction harmonic f=1.195 r0=3.76 { 6 601 }
interaction harmonic f=1.195 r0=3.76 { 6 602 }


# ------------------------------------------
# find stable situation first
conformation n=10000 error=1.0E-4 maxstep=2.5

# ------------------------------------------
# then setup a constant temperature
temperature k=3.166829379841521e-06 constant=293.0 tau=206.7055

# and finaly the dynamics statement, run 100 ps with steps of 0.1 fs
dynamics dt=4.13411 tend=4134110.5461 t=0.0 error=3.67493E-6








nate5@nate5:~$ sh b.sh
--2011-07-14 13:28:24-- http://boinc.gorlaeus.net/download/DownLoads/Standalone/Executables/Graphics/GLUT_ClassicalDynamics_Linux.x
Resolving boinc.gorlaeus.net... 132.229.173.85, 132.229.173.84
Connecting to boinc.gorlaeus.net|132.229.173.85|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 298408 (291K) [text/plain]
Saving to: `GLUT_ClassicalDynamics_Linux.x'

100%[==============================================================================================================================>] 298,408 251K/s in 1.2s

2011-07-14 13:28:26 (251 KB/s) - `GLUT_ClassicalDynamics_Linux.x' saved [298408/298408]

--2011-07-14 13:28:26-- http://boinc.gorlaeus.net/download/DownLoads/Standalone/Examples/hexane
Resolving boinc.gorlaeus.net... 132.229.173.84, 132.229.173.85
Connecting to boinc.gorlaeus.net|132.229.173.84|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 6442 (6.3K) [text/plain]
Saving to: `hexane'

100%[==============================================================================================================================>] 6,442 39.0K/s in 0.2s

2011-07-14 13:28:27 (39.0 KB/s) - `hexane' saved [6442/6442]

linux-gate.so.1 => (0xf77a9000)
libglut.so.3 => /usr/lib32/libglut.so.3 (0xf774f000)
libGLU.so.1 => /usr/lib32/libGLU.so.1 (0xf76e2000)
libGL.so.1 => /usr/lib32/mesa/libGL.so.1 (0xf768c000)
libXmu.so.6 => /usr/lib32/libXmu.so.6 (0xf7676000)
libXt.so.6 => /usr/lib32/libXt.so.6 (0xf7624000)
libXext.so.6 => /usr/lib32/libXext.so.6 (0xf7615000)
libXi.so.6 => /usr/lib32/libXi.so.6 (0xf7605000)
libSM.so.6 => /usr/lib32/libSM.so.6 (0xf75fd000)
libICE.so.6 => /usr/lib32/libICE.so.6 (0xf75e5000)
libX11.so.6 => /usr/lib32/libX11.so.6 (0xf74ca000)
libstdc++.so.6 => /usr/lib32/libstdc++.so.6 (0xf73df000)
libm.so.6 => /lib32/libm.so.6 (0xf73b9000)
libgcc_s.so.1 => /usr/lib32/libgcc_s.so.1 (0xf739c000)
libpthread.so.0 => /lib32/libpthread.so.0 (0xf7383000)
libc.so.6 => /lib32/libc.so.6 (0xf7226000)
libXdamage.so.1 => /usr/lib32/libXdamage.so.1 (0xf7222000)
libXfixes.so.3 => /usr/lib32/libXfixes.so.3 (0xf721c000)
libXxf86vm.so.1 => /usr/lib32/libXxf86vm.so.1 (0xf7215000)
libdrm.so.2 => /lib32/libdrm.so.2 (0xf720b000)
libdl.so.2 => /lib32/libdl.so.2 (0xf7207000)
/lib/ld-linux.so.2 (0xf77aa000)
libuuid.so.1 => /lib32/libuuid.so.1 (0xf7202000)
libxcb.so.1 => /usr/lib32/libxcb.so.1 (0xf71e9000)
librt.so.1 => /lib32/librt.so.1 (0xf71df000)
libXau.so.6 => /usr/lib32/libXau.so.6 (0xf71db000)
libXdmcp.so.6 => /usr/lib32/libXdmcp.so.6 (0xf71d5000)
b.sh: 4: ./GLUT_ClassicalDynamics_Linux.x: Permission denied
nate5@nate5:~$

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Message 2740 - Posted 15 Jul 2011 6:09:33 UTC

Sorry my bad; try this:

$ wget http://boinc.gorlaeus.net/download/DownLoads/Standalone/Executables/Graphics/GLUT_ClassicalDynamics_Linux.x
$ wget http://boinc.gorlaeus.net/download/DownLoads/Standalone/Examples/hexane
$ ldd ./GLUT_ClassicalDynamics_Linux.x
$ chmod +x ./GLUT_ClassicalDynamics_Linux.x
$ ./GLUT_ClassicalDynamics_Linux.x hexane

There is now an extra line to make the GLUT_ClassicalDynamics_Linux.x executable just before invoking it.


m.


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Message 2744 - Posted 15 Jul 2011 21:14:17 UTC - in response to Message ID 2740.

# a simple hexane molecule is being investigated.

# first define some colors
color id=0 rgb=[1.0,1.0,1.0]
color id=1 rgb=[1.0,0.0,0.0]
color id=2 rgb=[0.0,1.0,0.0]
color id=3 rgb=[0.0,0.0,1.0]
color id=4 rgb=[0.3,0.3,0.3]

# define the box
box cell=[25,25,25]

# ------------------------------------------
# the carbon chain
scale x=1.5 y=1.5 z=1.5
particle m=21894.71 q=6.0 r=1.46 p=[0.0,0.0,0.0] x=[-4.0,0.0,0.0] c=4 id=1
particle x=[-2.0,0.0,0.0]
particle x=[0.0,0.0,0.0]
particle x=[2.0,0.0,0.0]
particle x=[4.0,0.0,0.0]
particle x=[6.0,0.0,0.0]

# the bonding forces between the carbons
interaction harmonic f=1.275 r0=2.89 { 1 2 }
interaction harmonic f=1.275 r0=2.89 { 2 3 }
interaction harmonic f=1.275 r0=2.89 { 3 4 }
interaction harmonic f=1.275 r0=2.89 { 4 5 }
interaction harmonic f=1.275 r0=2.89 { 5 6 }

# the bond bending forces between the carbons
interaction bending f=0.175 deg=112.4 { 1 2 3 4 5 6}

# then the torsional force between the carbons
interaction torsional f=0.0175 n=1 deg=180.0 { 1 2 3 4 5 6}


# ------------------------------------------
# now for the hydrogen atoms on C1
translate x=-4.0
scale x=2.25 y=2.25 z=2.25
particle m=1827.81 q=1.0 r=0.701 p=[0.0,0.0,0.0] x=[1.0,0.0,0.0] c=0 id=100
particle x=[0.0,1.0,0.0]
particle x=[0.0,0.0,1.0]

# the H-C-H bending forces of the first CH3
interaction bending f=0.175 deg=107.7 { 100 1 101 }
interaction bending f=0.175 deg=107.7 { 101 1 102 }
interaction bending f=0.175 deg=107.7 { 102 1 100 }

#the H-C-C bending forces of the first CH3
interaction bending f=0.175 deg=111.2 { 2 1 100 }
interaction bending f=0.175 deg=111.2 { 2 1 101 }
interaction bending f=0.175 deg=111.2 { 2 1 102 }

# the bonding interactions of the first CH3
interaction harmonic f=1.195 r0=3.76 { 1 100 }
interaction harmonic f=1.195 r0=3.76 { 1 101 }
interaction harmonic f=1.195 r0=3.76 { 1 102 }


# ------------------------------------------
# now for the hydrogen atoms on C2
translate x=-2.0
scale x=2.25 y=2.25 z=2.25
particle x=[1.0,0.0,0.0] id=200
particle x=[0.0,1.0,0.0]

# the CH2 H-C-H bending on C2
interaction bending f=0.175 deg=106.1 { 200 2 201 }

# the four CH2 C-C-H bending on C2
interaction bending f=0.175 deg=109.5 { 1 2 200 }
interaction bending f=0.175 deg=109.5 { 1 2 201 }
interaction bending f=0.175 deg=109.5 { 3 2 200 }
interaction bending f=0.175 deg=109.5 { 3 2 201 }

# the bonding interactions of the first CH2 on C2
interaction harmonic f=1.195 r0=3.76 { 2 200 }
interaction harmonic f=1.195 r0=3.76 { 2 201 }


# ------------------------------------------
# now for the hydrogen atoms on C3
translate x=0.0
scale x=2.25 y=2.25 z=2.25
particle x=[1.0,0.0,0.0] id=300
particle x=[0.0,1.0,0.0]

# the CH2 H-C-H bending on C3
interaction bending f=0.175 deg=106.1 { 300 3 301 }

# the four CH2 C-C-H bending on C3
interaction bending f=0.175 deg=109.5 { 2 3 300 }
interaction bending f=0.175 deg=109.5 { 2 3 301 }
interaction bending f=0.175 deg=109.5 { 4 3 300 }
interaction bending f=0.175 deg=109.5 { 4 3 301 }

# the bonding interactions of the second CH2 on C3
interaction harmonic f=1.195 r0=3.76 { 3 300 }
interaction harmonic f=1.195 r0=3.76 { 3 301 }


# ------------------------------------------
# now for the hydrogen atoms on C4
translate x=2.0
scale x=2.25 y=2.25 z=2.25
particle x=[1.0,0.0,0.0] id=400
particle x=[0.0,1.0,0.0]

# the CH2 H-C-H bending on C4
interaction bending f=0.175 deg=106.1 { 400 4 401 }

# the four CH2 C-C-H bending on C4
interaction bending f=0.175 deg=109.5 { 3 4 400 }
interaction bending f=0.175 deg=109.5 { 3 4 401 }
interaction bending f=0.175 deg=109.5 { 5 4 400 }
interaction bending f=0.175 deg=109.5 { 5 4 401 }

# the bonding interactions of the second CH2 on C3
interaction harmonic f=1.195 r0=3.76 { 4 400 }
interaction harmonic f=1.195 r0=3.76 { 4 401 }


# ------------------------------------------
# now for the hydrogen atoms on C5
translate x=4.0
scale x=2.25 y=2.25 z=2.25
particle x=[1.0,0.0,0.0] id=500
particle x=[0.0,1.0,0.0]

# the CH2 H-C-H bending on C5
interaction bending f=0.175 deg=106.1 { 500 5 501 }

# the four CH2 C-C-H bending on C5
interaction bending f=0.175 deg=109.5 { 4 5 500 }
interaction bending f=0.175 deg=109.5 { 4 5 501 }
interaction bending f=0.175 deg=109.5 { 6 5 500 }
interaction bending f=0.175 deg=109.5 { 6 5 501 }

# the bonding interactions of the second CH2 on C5
interaction harmonic f=1.195 r0=3.76 { 5 500 }
interaction harmonic f=1.195 r0=3.76 { 5 501 }


# ------------------------------------------
# now for the hydrogen atoms on C6
translate x=6.0
scale x=2.25 y=2.25 z=2.25
particle x=[1.0,0.0,0.0] id=600
particle x=[0.0,1.0,0.0]
particle x=[0.0,0.0,1.0]

# the H-C-H bending forces of the second CH3
interaction bending f=0.175 deg=107.7 { 600 6 601 }
interaction bending f=0.175 deg=107.7 { 601 6 602 }
interaction bending f=0.175 deg=107.7 { 602 6 600 }

#the H-C-C bending forces of the second CH3
interaction bending f=0.175 deg=111.2 { 5 6 600 }
interaction bending f=0.175 deg=111.2 { 5 6 601 }
interaction bending f=0.175 deg=111.2 { 5 6 602 }

# the bonding interactions of the first CH3
interaction harmonic f=1.195 r0=3.76 { 6 600 }
interaction harmonic f=1.195 r0=3.76 { 6 601 }
interaction harmonic f=1.195 r0=3.76 { 6 602 }


# ------------------------------------------
# find stable situation first
conformation n=10000 error=1.0E-4 maxstep=2.5

# ------------------------------------------
# then setup a constant temperature
temperature k=3.166829379841521e-06 constant=293.0 tau=206.7055

# and finaly the dynamics statement, run 100 ps with steps of 0.1 fs
dynamics dt=4.13411 tend=4134110.5461 t=0.0 error=3.67493E-6



--2011-07-15 17:07:41-- http://boinc.gorlaeus.net/download/DownLoads/Standalone/Executables/Graphics/GLUT_ClassicalDynamics_Linux.x
Resolving boinc.gorlaeus.net... 132.229.173.85, 132.229.173.84
Connecting to boinc.gorlaeus.net|132.229.173.85|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 298408 (291K) [text/plain]
Saving to: `GLUT_ClassicalDynamics_Linux.x'

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2011-07-15 17:07:43 (249 KB/s) - `GLUT_ClassicalDynamics_Linux.x' saved [298408/298408]

--2011-07-15 17:07:43-- http://boinc.gorlaeus.net/download/DownLoads/Standalone/Examples/hexane
Resolving boinc.gorlaeus.net... 132.229.173.84, 132.229.173.85
Connecting to boinc.gorlaeus.net|132.229.173.84|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 6442 (6.3K) [text/plain]
Saving to: `hexane'

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2011-07-15 17:07:44 (40.6 KB/s) - `hexane' saved [6442/6442]

linux-gate.so.1 => (0xf76fc000)
libglut.so.3 => /usr/lib32/libglut.so.3 (0xf76a2000)
libGLU.so.1 => /usr/lib32/libGLU.so.1 (0xf7635000)
libGL.so.1 => /usr/lib32/mesa/libGL.so.1 (0xf75df000)
libXmu.so.6 => /usr/lib32/libXmu.so.6 (0xf75c9000)
libXt.so.6 => /usr/lib32/libXt.so.6 (0xf7577000)
libXext.so.6 => /usr/lib32/libXext.so.6 (0xf7568000)
libXi.so.6 => /usr/lib32/libXi.so.6 (0xf7558000)
libSM.so.6 => /usr/lib32/libSM.so.6 (0xf7550000)
libICE.so.6 => /usr/lib32/libICE.so.6 (0xf7538000)
libX11.so.6 => /usr/lib32/libX11.so.6 (0xf741d000)
libstdc++.so.6 => /usr/lib32/libstdc++.so.6 (0xf7332000)
libm.so.6 => /lib32/libm.so.6 (0xf730c000)
libgcc_s.so.1 => /usr/lib32/libgcc_s.so.1 (0xf72ef000)
libpthread.so.0 => /lib32/libpthread.so.0 (0xf72d6000)
libc.so.6 => /lib32/libc.so.6 (0xf7179000)
libXdamage.so.1 => /usr/lib32/libXdamage.so.1 (0xf7175000)
libXfixes.so.3 => /usr/lib32/libXfixes.so.3 (0xf716f000)
libXxf86vm.so.1 => /usr/lib32/libXxf86vm.so.1 (0xf7168000)
libdrm.so.2 => /lib32/libdrm.so.2 (0xf715e000)
libdl.so.2 => /lib32/libdl.so.2 (0xf715a000)
/lib/ld-linux.so.2 (0xf76fd000)
libuuid.so.1 => /lib32/libuuid.so.1 (0xf7155000)
libxcb.so.1 => /usr/lib32/libxcb.so.1 (0xf713c000)
librt.so.1 => /lib32/librt.so.1 (0xf7132000)
libXau.so.6 => /usr/lib32/libXau.so.6 (0xf712e000)
libXdmcp.so.6 => /usr/lib32/libXdmcp.so.6 (0xf7128000)
Starting the conformational search:

Max number of steps: 10000
Max step size: 2.50000000000000000000e+00
Max error for convergence: 1.00000000000000004792e-04

Total potential energy of system at start of search: 2.60251186644098559952e+01
Mean of distance squared of system at start of search: 6.67687499999999971578e+01

Conformation searcher stopped at itteration: 717

Total potential energy of system: 1.22756933999802600455e-01

Center of mass of system: [1.18693160475626219324e-07,3.14006397116209648334e-08,-5.81788785734016603686e-09]
Dipole moment of system: [1.16427589790061418284e+02,2.27075278706383123506e+01,4.43024118235498498564e+00]
Mean of distance squared of system: 4.19162706953920718433e+01

Starting the dynamical simulation:

Single cell: [2.50000000000000000000e+01,2.50000000000000000000e+01,2.50000000000000000000e+01]
Start time: 0.00000000000000000000e+00
End time: 4.13411054609999991953e+06
Max time step: 4.13410999999999972943e+00
Number of automatic snapshots to take in this run: 0
The boltzmann constant: 3.16682937984152115775e-06
The temperature will be kept constant at: 2.93000000000000000000e+02
The temperature rescaling time: 2.06705500000000000682e+02
The temperature random momenta factor: 0.00000000000000000000e+00
The temperature center of mass removal factor: 0.00000000000000000000e+00
The temperature langevin gamma factor: 0.00000000000000000000e+00

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Message 2745 - Posted 19 Jul 2011 5:51:14 UTC

So the application worked just fine and I think you saw the simulation run on screen; right?

m.

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Message 2746 - Posted 19 Jul 2011 17:07:37 UTC - in response to Message ID 2745.

So the application worked just fine and I think you saw the simulation run on screen; right?

m.


yep, so where am I going wrong?

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Message 2747 - Posted 20 Jul 2011 6:03:04 UTC

I think you found an issue with the boinc client software perhaps?

To be realy precise you could try the executable http://boinc.gorlaeus.net/download/BOINC_ClassicalDynamics_Linux.x as well with the 'hexane' input. If that also works them I'm sure it is a client issue.

The next step could then be trying the ubuntu 10.04.2 (LTS) live CD on one of those problematic hosts and install and test the boinc from the ubuntu repository from within the live CD environment (not installing ubunu on your host).

m.

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Message 2748 - Posted 20 Jul 2011 12:05:33 UTC - in response to Message ID 2747.

I think you found an issue with the boinc client software perhaps?

To be realy precise you could try the executable http://boinc.gorlaeus.net/download/BOINC_ClassicalDynamics_Linux.x as well with the 'hexane' input. If that also works them I'm sure it is a client issue.

m.


well that ran ok, saw the picture at the end. next is the live cd, that will be a while, got a 600 hour plus work unit going on right now. on both intel computers. the 4 amd are still running good on the project with no problem. should have known when I attached this project to the intel computer and got the ci//cgi error things would not go well...
thanks for all your help.. but for right now I'll leave the intel computer detached..

thanks again. sorry to be a pain, just got fed up with hitting my head against the wall on this one.

thanks for your help.

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Message 2749 - Posted 22 Jul 2011 6:10:24 UTC

Like I stated; it is a problem in the BOINC client; not in this pojects code; that runs fine. Also it is not a problem on the server. The cgi cg issue was also found to be an error in xml parsing of the client and as far as I know has been resolved in the newer clients. Please try again with a different client.

m.



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Message 2750 - Posted 22 Jul 2011 8:40:59 UTC - in response to Message ID 2749.

.. or it's a problem with the kernel. Seeing how 3 different Linux versions, with 3 different clients have similar errors --all with kernel 2.6.3x, while kernel 2.6.18 seems to work through it without a problem-- tells me something else is afoot.

Is it possible later kernels moved libraries around, so they're now out of the main path?
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Message 2751 - Posted 26 Jul 2011 5:53:37 UTC

And my test with ubuntu LTS 10.04.2 last week (kernel 2.6.32) on Intel cpus (Dell optiplex something) worked just fine with the BOINC client straight from the repository. The scientific code is just fine (he tested that specifically, and I can assure you we get valid results from most volunteers ;-)); there is yet again a bug in the BOINC client software I'm afraid...

m.
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Message 2752 - Posted 26 Jul 2011 12:22:35 UTC - in response to Message ID 2751.

And my test with ubuntu LTS 10.04.2 last week (kernel 2.6.32) on Intel cpus (Dell optiplex something) worked just fine with the BOINC client straight from the repository. The scientific code is just fine (he tested that specifically, and I can assure you we get valid results from most volunteers ;-)); there is yet again a bug in the BOINC client software I'm afraid...

m.


yesterday I got the chance to install the ubuntu LTS on the intel computer, and they ran all the way to the end, 100% and errored out with file transfer errors.
I also started looking at the other failed work units. Seems the amd cpu are failing because of a missing file from glut. linux os.. the inetl chips failing were all celeron chips, as far as I can see. So there is something about the celeron cpus, or it's something having to do with the timming of, or something to do with the output file transfer that is causing the file transfer error.
just what I've been able to see so far.

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Message 2753 - Posted 26 Jul 2011 13:59:44 UTC - in response to Message ID 2751.

...there is yet again a bug in the BOINC client software I'm afraid...

That's too easily said.
One task with multiple clients: http://boinc.gorlaeus.net/workunit.php?wuid=13521582

<core_client_version>6.10.58</core_client_version> had no problem.
Kernel version 2.6.39.3-SuSE11.4-pubserv1

<core_client_version>6.10.59</core_client_version> had error -161 (meaning that file(name)s aren't written to the client_state.xml file).
Kernel version 2.6.38-8-server

<core_client_version>6.2.14</core_client_version> had an error while loading shared libraries: libglut.so.3
Kernel version 2.6.33.5-xxxx-grs-ipv4-64

<core_client_version>6.10.58</core_client_version> also had error -161 (meaning that file(name)s aren't written to the client_state.xml file).
Kernel version 2.6.32-33-generic

Next example: http://boinc.gorlaeus.net/workunit.php?wuid=13504741

<core_client_version>6.10.58</core_client_version> had no problem.
Kernel version 2.6.39.3-SuSE11.4-pubserv1

<core_client_version>6.10.17</core_client_version> had an error while loading shared libraries: libglut.so.3
Kernel version 2.6.32-31-generic

<core_client_version>6.10.59</core_client_version> had error -161.
kernel version 2.6.38-8-server

<core_client_version>6.10.58</core_client_version> had no problem.
2.6.18-238.19.1.el5

Just showing that it's all kinds of different BOINC versions out there and that they all have either success or failure. It's more something of a (dynamic) library that isn't in place, between Linux kernel versions.
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Message 2754 - Posted 27 Jul 2011 6:08:07 UTC

1) In my experience; when a shared library is not loadable; the executable is not even started. Try this yourself; download the Leiden Classical app; run ldd on it; move one of them libraries (i.e. the freeglut one so the rest of your system doesn't stop ;-)) and run ldd again and try running the executable.

2) Different error messages do not automatically mean different bugs and it is also a false assumption thinking you are dealing with one and the same problem in all these examples. i.e. the missing of glut is a known error and therefore a special page has been setup to inform volunteers of this project on which libs to instal. When this problem happens; the simple test of running the scientific application without the BOINC client also fails (due to a missing .so) and earlier tests in this thread have shown this *not* to be the case. On his test systems (all intel's) the scientific Leiden Classical app ran fine with graphics and all without the BOINC client. Conclusions; a) There is no .so missing for the scientific Leiden Classical app. b) The Leiden Classical app itself runs just fine on intel. In another test I did myself; using Ubuntu LTS 10.04.2 on a 2.6.32 kernel on an Intel again showed a fully working setup. The problem is not reproducible off-site (so far).

3) The examples of errors you show could very well also be because of failing hardware or due to people overclocking or something like that. The only thing I can say here is that server side I have not detected any increase in problems appart from the ussual 'noise' all projects have (especially when using HR). From my epxerience when power units are to tight; memomory is failing or once in a while a fabrication error in a mainboard all can cause very strange and unpredictable errors. We have about 200 nodes in clusters here giving me that epxerience in the last 10 years.

4) the 'ci'/'cgi' string issue he also discoverd was traced back to an error in the xml parsing code of the BOINC client trying to remove spaces from a string some time ago.

All signs seem to point into the 'bad BOINC client' direction and as a test to check the hardware; I already proposed pushing in the Ubuntu Live CD which just ran fine here. If then things work; one can conclude it is not purely the hardware and definately not the science Leiden Classical application (they did not change in the test). Leaves a BOINC client (specific version) and or the system itself as the culprit(s). Next step is to run the SAME BOINC client from the Ubuntu CD on his OS. My gut feeling; I bet it is the client ;-) just based on track-record and a lack of quality control at Berkely compared to distro building groups with far more resources.

m.
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Message 2755 - Posted 30 Jul 2011 22:25:16 UTC - in response to Message ID 2754.

I think I got the problem fixed. I installed the 32 bit version of ubuntu 11.04
did a live cd first, loaded in freegult3 via console. installed boinc and attached this project, it ran no errors, I let it run 2 work units and both were good. at that point I install it on the intel computers both of them and attached this project to both intel celeron, did not get any ci//cgi error it hooked right up and downloaded work units and ran no problem. infact late 27th till late 29 ever one of the wu were good.
looks to me, just my opinion that the 64 bit boinc, the 64 bit linux os seem to have a few problems with intel celeron cpu.
I did look at at other system listed that passed good work units and the intel cpu was 32 bit, or the 64 bit cpu was running 32 bit linux and 32 bit boinc.
I could be wrong only looked at about 12 or so.
but I do know for 2 days the 2 celeron cpu ran this project non stop without fail...


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