P6701 (Run 43, Clone 27, Gen 14) Water not settled

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tati
Posts: 21
Joined: Sat May 03, 2008 7:42 am
Hardware configuration: AMD Phenom II 940 Black Edition, 4GB RAM, Ubuntu 9.10 for SMP.
AMD Athlon XP 2400, 512MB RAM, Win XP+SP3 (and some other Intel P4-2,8 PC's for "classic" folding).
AMD Athlon64 3200 "Venice", 1GB RAM, Win XP+SP3, GeForce 9500GT for GPU and classic folding.
Location: Commuter between Herrenberg/Germany and Satu Mare/Romania

P6701 (Run 43, Clone 27, Gen 14) Water not settled

Post by tati »

Hi,

Often I experience the following situation:

Code: Select all

[05:07:00] - Looking at optimizations...
[05:07:00] - Created dyn
[05:07:00] - Files status OK
[05:07:00] - Expanded 763430 -> 1404481 (decompressed 183.9 percent)
[05:07:00] Called DecompressByteArray: compressed_data_size=763430 data_size=1404481, decompressed_data_size=1404481 diff=0
[05:07:00] - Digital signature verified
[05:07:00] 
[05:07:00] Project: 6701 (Run 43, Clone 27, Gen 14)
[05:07:00] 
[05:07:00] Assembly optimizations on if available.
[05:07:00] Entering M.D.
Starting 4 threads
NNODES=4, MYRANK=1, HOSTNAME=thread #1
NNODES=4, MYRANK=3, HOSTNAME=thread #3
NNODES=4, MYRANK=0, HOSTNAME=thread #0
NNODES=4, MYRANK=2, HOSTNAME=thread #2
Reading file work/wudata_09.tpr, VERSION 4.0.99_development_20090605 (single precision)
Making 1D domain decomposition 4 x 1 x 1
starting mdrun 'VSD in POPC and water, neutralized'
30000000 steps, 150000.0 ps (continuing from step 28000000, 140000.0 ps).

step 28000000: Water molecule starting at atom 24076 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Step 28000001  Warning: pressure scaling more than 1%, mu: 1.02169 1.02169 1.00829

Step 28000001  Warning: pressure scaling more than 1%, mu: 1.02169 1.02169 1.00829

Step 28000001  Warning: pressure scaling more than 1%, mu: 1.02169 1.02169 1.00829

Step 28000001  Warning: pressure scaling more than 1%, mu: 1.02169 1.02169 1.00829

step 28000001: Water molecule starting at atom 24076 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 28000001: Water molecule starting at atom 25228 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Segmentation fault
[05:07:07] Completed 0 out of 2000000 steps  (0%)
[05:07:07] CoreStatus = 8B (139)
[05:07:07] Client-core communications error: ERROR 0x8b
[05:07:07] Deleting current work unit & continuing...
[05:07:41] Trying to send all finished work units
[05:07:41] + No unsent completed units remaining.
[05:07:41] - Preparing to get new work unit...
[05:07:41] Cleaning up work directory
[05:07:41] + Attempting to get work packet
[05:07:41] Passkey found
[05:07:41] - Will indicate memory of 3710 MB
[05:07:41] - Connecting to assignment server
[05:07:41] Connecting to http://assign.stanford.edu:8080/
[05:07:42] Posted data.
[05:07:42] Initial: 40AB; - Successful: assigned to (171.64.65.56).
[05:07:42] + News From Folding@Home: Welcome to Folding@Home
[05:07:42] Loaded queue successfully.
[05:07:42] Connecting to http://171.64.65.56:8080/
[05:07:43] Posted data.
[05:07:43] Initial: 0000; - Receiving payload (expected size: 763942)
[05:07:45] - Downloaded at ~373 kB/s
[05:07:45] - Averaged speed for that direction ~374 kB/s
[05:07:45] + Received work.
[05:07:45] + Closed connections
[05:07:50] 
[05:07:50] + Processing work unit
[05:07:50] Core required: FahCore_a3.exe
[05:07:50] Core found.
[05:07:50] Working on queue slot 00 [July 17 05:07:50 UTC]
[05:07:50] + Working ...
[05:07:50] - Calling './FahCore_a3.exe -dir work/ -nice 19 -suffix 00 -np 4 -checkpoint 15 -verbose -lifeline 2098 -version 629'

[05:07:50] 
[05:07:50] *------------------------------*
[05:07:50] Folding@Home Gromacs SMP Core
[05:07:50] Version 2.22 (June 10, 2010)
[05:07:50] 
[05:07:50] Preparing to commence simulation
[05:07:50] - Looking at optimizations...
[05:07:50] - Created dyn
[05:07:50] - Files status OK
[05:07:50] - Expanded 763430 -> 1404481 (decompressed 183.9 percent)
[05:07:50] Called DecompressByteArray: compressed_data_size=763430 data_size=1404481, decompressed_data_size=1404481 diff=0
[05:07:50] - Digital signature verified
[05:07:50] 
[05:07:50] Project: 6701 (Run 43, Clone 27, Gen 14)
[05:07:50] 
[05:07:50] Assembly optimizations on if available.
[05:07:50] Entering M.D.
Starting 4 threads
NNODES=4, MYRANK=0, HOSTNAME=thread #0
NNODES=4, MYRANK=3, HOSTNAME=thread #3
NNODES=4, MYRANK=1, HOSTNAME=thread #1
NNODES=4, MYRANK=2, HOSTNAME=thread #2
Reading file work/wudata_00.tpr, VERSION 4.0.99_development_20090605 (single precision)
Making 1D domain decomposition 4 x 1 x 1
starting mdrun 'VSD in POPC and water, neutralized'
30000000 steps, 150000.0 ps (continuing from step 28000000, 140000.0 ps).

step 28000000: Water molecule starting at atom 24076 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Step 28000001  Warning: pressure scaling more than 1%, mu: 1.02169 1.02169 1.00829

Step 28000001  Warning: pressure scaling more than 1%, mu: 1.02169 1.02169 1.00829

Step 28000001  Warning: pressure scaling more than 1%, mu: 1.02169 1.02169 1.00829

Step 28000001  Warning: pressure scaling more than 1%, mu: 1.02169 1.02169 1.00829

step 28000001: Water molecule starting at atom 28600 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 28000001: Water molecule starting at atom 13300 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Segmentation fault
[05:07:57] Completed 0 out of 2000000 steps  (0%)
[05:07:57] CoreStatus = 8B (139)
[05:07:57] Client-core communications error: ERROR 0x8b
[05:07:57] - Attempting to download new core...
[05:07:57] + Downloading new core: FahCore_a3.exe
[05:07:57] Downloading core (/~pande/Linux/AMD64/Core_a3.fah from www.stanford.edu)
[05:07:58] Initial: AFDE; + 10240 bytes downloaded
[05:07:58] Initial: 0746; + 20480 bytes downloaded
[05:07:59] Initial: 8639; + 30720 bytes downloaded
[05:07:59] Initial: C217; + 40960 bytes downloaded
[05:07:59] Initial: 994A; + 51200 bytes downloaded
[05:07:59] Initial: 41DB; + 61440 bytes downloaded
[05:07:59] Initial: EDA4; + 71680 bytes downloaded
[05:07:59] Initial: 0524; + 81920 bytes downloaded
[05:07:59] Initial: B692; + 92160 bytes downloaded
[05:07:59] Initial: 9BFD; + 102400 bytes downloaded
[05:07:59] Initial: 683C; + 112640 bytes downloaded
[05:07:59] Initial: 2B9F; + 122880 bytes downloaded
[05:07:59] Initial: 125C; + 133120 bytes downloaded
[05:07:59] Initial: 262F; + 143360 bytes downloaded
[05:07:59] Initial: EEC2; + 153600 bytes downloaded
[05:07:59] Initial: 52D5; + 163840 bytes downloaded
[05:07:59] Initial: 036C; + 174080 bytes downloaded
[05:07:59] Initial: B048; + 184320 bytes downloaded
[05:07:59] Initial: 8923; + 194560 bytes downloaded
[05:07:59] Initial: 60A8; + 204800 bytes downloaded
[05:07:59] Initial: 33DF; + 215040 bytes downloaded
[05:07:59] Initial: FA5F; + 225280 bytes downloaded
[05:07:59] Initial: C8D3; + 235520 bytes downloaded
[05:07:59] Initial: C801; + 245760 bytes downloaded
[05:07:59] Initial: 5A86; + 256000 bytes downloaded
[05:07:59] Initial: CC0C; + 266240 bytes downloaded
[05:07:59] Initial: BD63; + 276480 bytes downloaded
[05:07:59] Initial: E39E; + 286720 bytes downloaded
[05:07:59] Initial: 54EB; + 296960 bytes downloaded
[05:07:59] Initial: 93CD; + 307200 bytes downloaded
[05:08:00] Initial: 2C68; + 317440 bytes downloaded
[05:08:00] Initial: F121; + 327680 bytes downloaded
[05:08:00] Initial: 5843; + 337920 bytes downloaded
[05:08:00] Initial: D14A; + 348160 bytes downloaded
[05:08:00] Initial: B1E3; + 358400 bytes downloaded
[05:08:00] Initial: C8A2; + 368640 bytes downloaded
[05:08:00] Initial: 801B; + 378880 bytes downloaded
[05:08:00] Initial: 62BD; + 389120 bytes downloaded
[05:08:00] Initial: C995; + 399360 bytes downloaded
[05:08:00] Initial: 1E4F; + 409600 bytes downloaded
[05:08:00] Initial: E666; + 419840 bytes downloaded
[05:08:00] Initial: 1637; + 430080 bytes downloaded
[05:08:00] Initial: EF41; + 440320 bytes downloaded
[05:08:00] Initial: 0F67; + 450560 bytes downloaded
[05:08:00] Initial: 8BA8; + 460800 bytes downloaded
[05:08:00] Initial: 7D30; + 471040 bytes downloaded
[05:08:00] Initial: 8F72; + 481280 bytes downloaded
[05:08:00] Initial: EDB2; + 491520 bytes downloaded
[05:08:00] Initial: BA84; + 501760 bytes downloaded
[05:08:00] Initial: 300D; + 512000 bytes downloaded
[05:08:00] Initial: 262F; + 522240 bytes downloaded
[05:08:00] Initial: CAA1; + 532480 bytes downloaded
[05:08:00] Initial: 3061; + 542720 bytes downloaded
[05:08:00] Initial: 7DF0; + 552960 bytes downloaded
[05:08:00] Initial: 6796; + 563200 bytes downloaded
[05:08:00] Initial: A0C0; + 573440 bytes downloaded
[05:08:00] Initial: 3293; + 583680 bytes downloaded
[05:08:00] Initial: 6BC0; + 593920 bytes downloaded
[05:08:00] Initial: 8385; + 604160 bytes downloaded
[05:08:00] Initial: 8F3F; + 614400 bytes downloaded
[05:08:00] Initial: CFCC; + 624640 bytes downloaded
[05:08:00] Initial: F554; + 634880 bytes downloaded
[05:08:00] Initial: 7EBD; + 645120 bytes downloaded
[05:08:00] Initial: 20D8; + 655360 bytes downloaded
[05:08:00] Initial: CD82; + 665600 bytes downloaded
[05:08:00] Initial: 5927; + 675840 bytes downloaded
[05:08:00] Initial: DDD1; + 686080 bytes downloaded
[05:08:00] Initial: D3C0; + 696320 bytes downloaded
[05:08:00] Initial: 3FFA; + 706560 bytes downloaded
[05:08:00] Initial: D2D8; + 716800 bytes downloaded
[05:08:00] Initial: CE94; + 727040 bytes downloaded
[05:08:00] Initial: A06A; + 737280 bytes downloaded
[05:08:00] Initial: A3C4; + 747520 bytes downloaded
[05:08:00] Initial: 3119; + 757760 bytes downloaded
[05:08:00] Initial: 9631; + 768000 bytes downloaded
[05:08:00] Initial: 3D79; + 778240 bytes downloaded
[05:08:00] Initial: 0AAD; + 788480 bytes downloaded
[05:08:00] Initial: A6B7; + 798720 bytes downloaded
[05:08:00] Initial: 1D65; + 808960 bytes downloaded
[05:08:00] Initial: 2C08; + 819200 bytes downloaded
[05:08:00] Initial: AC56; + 829440 bytes downloaded
[05:08:00] Initial: 9632; + 839680 bytes downloaded
[05:08:00] Initial: F50A; + 849920 bytes downloaded
[05:08:00] Initial: D2D0; + 860160 bytes downloaded
[05:08:00] Initial: 9BAC; + 870400 bytes downloaded
[05:08:00] Initial: 744A; + 880640 bytes downloaded
[05:08:00] Initial: 265D; + 890880 bytes downloaded
[05:08:00] Initial: D54D; + 901120 bytes downloaded
[05:08:00] Initial: 2574; + 911360 bytes downloaded
[05:08:00] Initial: 09A7; + 921600 bytes downloaded
[05:08:00] Initial: 2769; + 931840 bytes downloaded
[05:08:00] Initial: 0235; + 942080 bytes downloaded
[05:08:00] Initial: 7ADA; + 952320 bytes downloaded
[05:08:00] Initial: 1276; + 962560 bytes downloaded
[05:08:00] Initial: 7DF8; + 972800 bytes downloaded
[05:08:00] Initial: F7DE; + 983040 bytes downloaded
[05:08:00] Initial: 4D4F; + 993280 bytes downloaded
[05:08:00] Initial: 35B5; + 1003520 bytes downloaded
[05:08:00] Initial: DE6D; + 1013760 bytes downloaded
[05:08:00] Initial: D000; + 1024000 bytes downloaded
[05:08:00] Initial: A810; + 1034240 bytes downloaded
[05:08:00] Initial: 339C; + 1044480 bytes downloaded
[05:08:00] Initial: AB07; + 1054720 bytes downloaded
[05:08:00] Initial: 88D8; + 1064960 bytes downloaded
[05:08:00] Initial: AC0E; + 1075200 bytes downloaded
[05:08:00] Initial: ACB6; + 1085440 bytes downloaded
[05:08:00] Initial: 1044; + 1095680 bytes downloaded
[05:08:00] Initial: 2854; + 1105920 bytes downloaded
[05:08:00] Initial: 8A45; + 1116160 bytes downloaded
[05:08:00] Initial: FBEC; + 1126400 bytes downloaded
[05:08:00] Initial: 996B; + 1136640 bytes downloaded
[05:08:00] Initial: 9EFE; + 1146880 bytes downloaded
[05:08:00] Initial: 71B9; + 1157120 bytes downloaded
[05:08:00] Initial: 9ED2; + 1167360 bytes downloaded
[05:08:00] Initial: FF0C; + 1177600 bytes downloaded
[05:08:00] Initial: 875C; + 1187840 bytes downloaded
[05:08:00] Initial: 5BC6; + 1198080 bytes downloaded
[05:08:00] Initial: 3A32; + 1208320 bytes downloaded
[05:08:00] Initial: 52FD; + 1218560 bytes downloaded
[05:08:00] Initial: 2003; + 1228800 bytes downloaded
[05:08:01] Initial: BBE1; + 1239040 bytes downloaded
[05:08:01] Initial: E32A; + 1249280 bytes downloaded
[05:08:01] Initial: 3018; + 1259520 bytes downloaded
[05:08:01] Initial: 4993; + 1269760 bytes downloaded
[05:08:01] Initial: 29B8; + 1280000 bytes downloaded
[05:08:01] Initial: 8500; + 1290240 bytes downloaded
[05:08:01] Initial: 187D; + 1300480 bytes downloaded
[05:08:01] Initial: 4A45; + 1310720 bytes downloaded
[05:08:01] Initial: F675; + 1320960 bytes downloaded
[05:08:01] Initial: 6375; + 1331200 bytes downloaded
[05:08:01] Initial: 6A5E; + 1341440 bytes downloaded
[05:08:01] Initial: A1B8; + 1351680 bytes downloaded
[05:08:01] Initial: 81F9; + 1361920 bytes downloaded
[05:08:01] Initial: 0F3E; + 1372160 bytes downloaded
[05:08:01] Initial: 492A; + 1382400 bytes downloaded
[05:08:01] Initial: 0C62; + 1392640 bytes downloaded
[05:08:01] Initial: 555C; + 1402880 bytes downloaded
[05:08:01] Initial: 04CC; + 1413120 bytes downloaded
[05:08:01] Initial: 79CE; + 1423360 bytes downloaded
[05:08:01] Initial: 11AE; + 1433600 bytes downloaded
[05:08:01] Initial: 28C3; + 1443840 bytes downloaded
[05:08:01] Initial: FA61; + 1454080 bytes downloaded
[05:08:01] Initial: E672; + 1464320 bytes downloaded
[05:08:01] Initial: 9449; + 1474560 bytes downloaded
[05:08:01] Initial: 97C8; + 1484800 bytes downloaded
[05:08:01] Initial: 1ABF; + 1495040 bytes downloaded
[05:08:01] Initial: 5BAB; + 1505280 bytes downloaded
[05:08:01] Initial: 4683; + 1515520 bytes downloaded
[05:08:01] Initial: F1D1; + 1525760 bytes downloaded
[05:08:01] Initial: 2593; + 1536000 bytes downloaded
[05:08:01] Initial: 8FBF; + 1546240 bytes downloaded
[05:08:01] Initial: 4D8E; + 1556480 bytes downloaded
[05:08:01] Initial: 18E9; + 1566720 bytes downloaded
[05:08:01] Initial: CDB8; + 1576960 bytes downloaded
[05:08:01] Initial: 1A06; + 1587200 bytes downloaded
[05:08:01] Initial: D9CB; + 1597440 bytes downloaded
[05:08:01] Initial: 7376; + 1607680 bytes downloaded
[05:08:01] Initial: 6AA5; + 1617920 bytes downloaded
[05:08:01] Initial: EFBE; + 1628160 bytes downloaded
[05:08:01] Initial: 2633; + 1638400 bytes downloaded
[05:08:01] Initial: 5867; + 1648640 bytes downloaded
[05:08:01] Initial: F056; + 1658880 bytes downloaded
[05:08:01] Initial: 1B0F; + 1669120 bytes downloaded
[05:08:01] Initial: A803; + 1679360 bytes downloaded
[05:08:01] Initial: 3C5B; + 1689600 bytes downloaded
[05:08:01] Initial: 0310; + 1699840 bytes downloaded
[05:08:01] Initial: DCF4; + 1710080 bytes downloaded
[05:08:01] Initial: 798F; + 1720320 bytes downloaded
[05:08:01] Initial: 09B3; + 1730560 bytes downloaded
[05:08:01] Initial: 5761; + 1740800 bytes downloaded
[05:08:01] Initial: 573E; + 1751040 bytes downloaded
[05:08:01] Initial: 5B17; + 1761280 bytes downloaded
[05:08:01] Initial: 2C66; + 1771520 bytes downloaded
[05:08:01] Initial: 68A2; + 1781760 bytes downloaded
[05:08:01] Initial: 5F08; + 1792000 bytes downloaded
[05:08:01] Initial: FD18; + 1802240 bytes downloaded
[05:08:01] Initial: 1B9B; + 1812480 bytes downloaded
[05:08:01] Initial: 306B; + 1822720 bytes downloaded
[05:08:01] Initial: E43E; + 1832960 bytes downloaded
[05:08:01] Initial: 2B7A; + 1843200 bytes downloaded
[05:08:01] Initial: E89D; + 1853440 bytes downloaded
[05:08:01] Initial: F503; + 1863680 bytes downloaded
[05:08:01] Initial: 6BEF; + 1873920 bytes downloaded
[05:08:01] Initial: 3937; + 1884160 bytes downloaded
[05:08:01] Initial: 1971; + 1894400 bytes downloaded
[05:08:01] Initial: 077E; + 1904640 bytes downloaded
[05:08:01] Initial: 14A1; + 1914880 bytes downloaded
[05:08:01] Initial: 6D08; + 1925120 bytes downloaded
[05:08:01] Initial: 98DB; + 1935360 bytes downloaded
[05:08:01] Initial: A832; + 1945600 bytes downloaded
[05:08:01] Initial: B69C; + 1955840 bytes downloaded
[05:08:01] Initial: 4C11; + 1966080 bytes downloaded
[05:08:01] Initial: 8EFE; + 1976320 bytes downloaded
[05:08:01] Initial: 965B; + 1986560 bytes downloaded
[05:08:01] Initial: 193C; + 1996800 bytes downloaded
[05:08:01] Initial: 6891; + 2007040 bytes downloaded
[05:08:01] Initial: 7870; + 2017280 bytes downloaded
[05:08:01] Initial: 3111; + 2027520 bytes downloaded
[05:08:01] Initial: C010; + 2037760 bytes downloaded
[05:08:01] Initial: 4AAB; + 2048000 bytes downloaded
[05:08:01] Initial: 1A4C; + 2058240 bytes downloaded
[05:08:01] Initial: 5CC2; + 2068480 bytes downloaded
[05:08:01] Initial: F05E; + 2078720 bytes downloaded
[05:08:01] Initial: E8C9; + 2088960 bytes downloaded
[05:08:01] Initial: 91BC; + 2099200 bytes downloaded
[05:08:01] Initial: F3FB; + 2109440 bytes downloaded
[05:08:01] Initial: 8C6E; + 2119680 bytes downloaded
[05:08:01] Initial: 6586; + 2129920 bytes downloaded
[05:08:01] Initial: 3BA5; + 2140160 bytes downloaded
[05:08:01] Initial: 4461; + 2150400 bytes downloaded
[05:08:01] Initial: 5656; + 2160640 bytes downloaded
[05:08:01] Initial: FF9B; + 2170880 bytes downloaded
[05:08:01] Initial: 9DD2; + 2181120 bytes downloaded
[05:08:01] Initial: FCD2; + 2191360 bytes downloaded
[05:08:01] Initial: A5FA; + 2201600 bytes downloaded
[05:08:01] Initial: DE1B; + 2211840 bytes downloaded
[05:08:01] Initial: 8D46; + 2222080 bytes downloaded
[05:08:01] Initial: 7880; + 2232320 bytes downloaded
[05:08:01] Initial: 6DFE; + 2242560 bytes downloaded
[05:08:01] Initial: 5966; + 2252800 bytes downloaded
[05:08:01] Initial: 8827; + 2263040 bytes downloaded
[05:08:01] Initial: DF4C; + 2268923 bytes downloaded
[05:08:01] Verifying core Core_a3.fah...
[05:08:01] Signature is VALID
[05:08:01] 
[05:08:01] Trying to unzip core FahCore_a3.exe
[05:08:02] Decompressed FahCore_a3.exe (5277040 bytes) successfully
[05:08:02] + Core successfully engaged
[05:08:25] Deleting current work unit & continuing...
[05:08:59] Trying to send all finished work units
[05:08:59] + No unsent completed units remaining.
[05:08:59] - Preparing to get new work unit...
[05:08:59] Cleaning up work directory
[05:08:59] + Attempting to get work packet
[05:08:59] Passkey found
[05:08:59] - Will indicate memory of 3710 MB
[05:08:59] - Connecting to assignment server
[05:08:59] Connecting to http://assign.stanford.edu:8080/
[05:09:00] Posted data.
[05:09:00] Initial: 40AB; - Successful: assigned to (171.64.65.56).
[05:09:00] + News From Folding@Home: Welcome to Folding@Home
[05:09:00] Loaded queue successfully.
[05:09:00] Connecting to http://171.64.65.56:8080/
[05:09:01] Posted data.
[05:09:01] Initial: 0000; - Receiving payload (expected size: 763942)
[05:09:03] - Downloaded at ~373 kB/s
[05:09:03] - Averaged speed for that direction ~373 kB/s
[05:09:03] + Received work.
[05:09:03] + Closed connections
[05:09:08] 
[05:09:08] + Processing work unit
[05:09:08] Core required: FahCore_a3.exe
[05:09:08] Core found.
[05:09:08] Working on queue slot 01 [July 17 05:09:08 UTC]
[05:09:08] + Working ...
[05:09:08] - Calling './FahCore_a3.exe -dir work/ -nice 19 -suffix 01 -np 4 -checkpoint 15 -verbose -lifeline 2098 -version 629'

[05:09:08] 
[05:09:08] *------------------------------*
[05:09:08] Folding@Home Gromacs SMP Core
[05:09:08] Version 2.22 (June 10, 2010)
[05:09:08] 
[05:09:08] Preparing to commence simulation
[05:09:08] - Looking at optimizations...
[05:09:08] - Created dyn
[05:09:08] - Files status OK
[05:09:08] - Expanded 763430 -> 1404481 (decompressed 183.9 percent)
[05:09:08] Called DecompressByteArray: compressed_data_size=763430 data_size=1404481, decompressed_data_size=1404481 diff=0
[05:09:08] - Digital signature verified
[05:09:08] 
[05:09:08] Project: 6701 (Run 43, Clone 27, Gen 14)
[05:09:08] 
[05:09:08] Assembly optimizations on if available.
[05:09:08] Entering M.D.
Starting 4 threads
NNODES=4, MYRANK=1, HOSTNAME=thread #1
NNODES=4, MYRANK=0, HOSTNAME=thread #0
NNODES=4, MYRANK=2, HOSTNAME=thread #2
NNODES=4, MYRANK=3, HOSTNAME=thread #3
Reading file work/wudata_01.tpr, VERSION 4.0.99_development_20090605 (single precision)
Making 1D domain decomposition 4 x 1 x 1
starting mdrun 'VSD in POPC and water, neutralized'
30000000 steps, 150000.0 ps (continuing from step 28000000, 140000.0 ps).

step 28000000: Water molecule starting at atom 24076 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Step 28000001  Warning: pressure scaling more than 1%, mu: 1.02169 1.02169 1.00829

Step 28000001  Warning: pressure scaling more than 1%, mu: 1.02169 1.02169 1.00829

Step 28000001  Warning: pressure scaling more than 1%, mu: 1.02169 1.02169 1.00829

Step 28000001  Warning: pressure scaling more than 1%, mu: 1.02169 1.02169 1.00829

step 28000001: Water molecule starting at atom 13300 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 28000001: Water molecule starting at atom 28600 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Segmentation fault
[05:09:15] Completed 0 out of 2000000 steps  (0%)
[05:09:15] CoreStatus = 8B (139)
[05:09:15] Client-core communications error: ERROR 0x8b
[05:09:15] Deleting current work unit & continuing...
[05:09:48] Trying to send all finished work units
[05:09:48] + No unsent completed units remaining.
[05:09:48] - Preparing to get new work unit...
[05:09:48] Cleaning up work directory
[05:09:48] + Attempting to get work packet
[05:09:48] Passkey found
[05:09:48] - Will indicate memory of 3710 MB
[05:09:48] - Connecting to assignment server
[05:09:48] Connecting to http://assign.stanford.edu:8080/
[05:09:49] Posted data.
[05:09:49] Initial: 40AB; - Successful: assigned to (171.64.65.54).
[05:09:49] + News From Folding@Home: Welcome to Folding@Home
[05:09:49] Loaded queue successfully.
[05:09:49] Connecting to http://171.64.65.54:8080/
[05:09:51] Posted data.
[05:09:51] Initial: 0000; - Receiving payload (expected size: 1763395)
[05:09:54] - Downloaded at ~574 kB/s
[05:09:54] - Averaged speed for that direction ~413 kB/s
[05:09:54] + Received work.
[05:09:54] + Closed connections
[05:09:59] 
[05:09:59] + Processing work unit
[05:09:59] Core required: FahCore_a3.exe
[05:09:59] Core found.
[05:09:59] Working on queue slot 02 [July 17 05:09:59 UTC]
[05:09:59] + Working ...
[05:09:59] - Calling './FahCore_a3.exe -dir work/ -nice 19 -suffix 02 -np 4 -checkpoint 15 -verbose -lifeline 2098 -version 629'

[05:09:59] 
[05:09:59] *------------------------------*
[05:09:59] Folding@Home Gromacs SMP Core
[05:09:59] Version 2.22 (June 10, 2010)
[05:09:59] 
[05:09:59] Preparing to commence simulation
[05:09:59] - Looking at optimizations...
[05:09:59] - Created dyn
[05:09:59] - Files status OK
[05:10:00] - Expanded 1762883 -> 2248557 (decompressed 127.5 percent)
[05:10:00] Called DecompressByteArray: compressed_data_size=1762883 data_size=2248557, decompressed_data_size=2248557 diff=0
[05:10:00] - Digital signature verified
[05:10:00] 
[05:10:00] Project: 6064 (Run 0, Clone 19, Gen 104)
[05:10:00] 
[05:10:00] Assembly optimizations on if available.
[05:10:00] Entering M.D.
Starting 4 threads
NNODES=4, MYRANK=0, HOSTNAME=thread #0
NNODES=4, MYRANK=3, HOSTNAME=thread #3
NNODES=4, MYRANK=1, HOSTNAME=thread #1
NNODES=4, MYRANK=2, HOSTNAME=thread #2
Reading file work/wudata_02.tpr, VERSION 4.0.99_development_20090605 (single precision)
Making 1D domain decomposition 1 x 4 x 1
starting mdrun 'Mutant_scan'
52500004 steps, 105000.0 ps (continuing from step 52000004, 104000.0 ps).
[05:10:06] Completed 0 out of 500000 steps  (0%)

NOTE: Turning on dynamic load balancing

[05:16:15] Completed 5000 out of 500000 steps  (1%)
[05:23:06] Completed 10000 out of 500000 steps  (2%)
[05:29:23] Completed 15000 out of 500000 steps  (3%)
[05:35:29] Completed 20000 out of 500000 steps  (4%)
The Linux/AMD64/Core_a3 core was downloaded many times before...
I have completed already many p6701 WU's with no problems.

System (dedicated exclusively to FAH with no other programs or applications):
Linux Ubuntu 9.10 kernel 2.6.31-19
AMD Phenom 940 on Asus M4A78 Pro board with 4GB RAM(dual channel)
Seagate 160 GB SATA
580W power supply.

Can somebody give an explanation?
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PantherX
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Re: Water molecule can not be settled

Post by PantherX »

If you have completed several WUs on the same machine, then it could be a Bad WU. You may want to rename the Thread to Project: 6701 (Run 43, Clone 27, Gen 14) and it would be moved to the Issues with specific a WU sub-forum by an Admin/Mod who will mark it as bad if other reports are found in the database.

EDIT - I am a Windows user so I am not sure if this is a Linux Specific error.
ETA:
Now ↞ Very Soon ↔ Soon ↔ Soon-ish ↔ Not Soon ↠ End Of Time

Welcome To The F@H Support Forum Ӂ Troubleshooting Bad WUs Ӂ Troubleshooting Server Connectivity Issues
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bruce
Posts: 20824
Joined: Thu Nov 29, 2007 10:13 pm
Location: So. Cal.

Re: Water molecule can not be settled

Post by bruce »

PantherX wrote:I am a Windows user so I am not sure if this is a Linux Specific error.
Nope. It's a Gromacs error which applies to any platform.

The WU (P6701,R43,C27,G14) has been reported as a bad WU
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