Project: 13860 (Run 0, Clone 3921, Gen 0)

[VulkanLogic]

Hello,

I think the frame0.tpr work file is corrupted.

getting different kinds of errors:
ERROR:wrong string length 0 for string buf (source /host/debian-stable-64bit-core-a7-avx-release/gromacs-core/build/gromacs/src/gromacs/fileio/tpxio.c, line 3206)

Unknown precision in file frame0.tpr: real is 549316104 bytes instead of 4 or 8

reading tpx file (frame0.tpr) version 549316480 with version 100 program

Can not read file frame0.tpr,
this file is from a Gromacs version which is older than 2.0
Make a new one with grompp or use a gro or pdb file, if possible

symtab get_symtab_handle 35184 not found


LOG:

Code: Select all

*********************** Log Started 2020-03-19T07:16:01Z ***********************
07:16:01:************************* Folding@home Client *************************
07:16:01:        Website: https://foldingathome.org/
07:16:01:      Copyright: (c) 2009-2018 foldingathome.org
07:16:01:         Author: Joseph Coffland <joseph@cauldrondevelopment.com>
07:16:01:           Args: 
07:16:01:         Config: /home/anon/config.xml
07:16:01:******************************** Build ********************************
07:16:01:        Version: 7.5.1
07:16:01:           Date: May 11 2018
07:16:01:           Time: 19:59:04
07:16:01:     Repository: Git
07:16:01:       Revision: 4705bf53c635f88b8fe85af7675557e15d491ff0
07:16:01:         Branch: master
07:16:01:       Compiler: GNU 6.3.0 20170516
07:16:01:        Options: -std=gnu++98 -O3 -funroll-loops
07:16:01:       Platform: linux2 4.14.0-3-amd64
07:16:01:           Bits: 64
07:16:01:           Mode: Release
07:16:01:******************************* System ********************************
07:16:01:            CPU: AMD Ryzen 7 3700X 8-Core Processor
07:16:01:         CPU ID: AuthenticAMD Family 23 Model 113 Stepping 0
07:16:01:           CPUs: 16
07:16:01:         Memory: 31.37GiB
07:16:01:    Free Memory: 1.15GiB
07:16:01:        Threads: POSIX_THREADS
07:16:01:     OS Version: 5.3
07:16:01:    Has Battery: false
07:16:01:     On Battery: false
07:16:01:     UTC Offset: 1
07:16:01:            PID: 22968
07:16:01:            CWD: /home/anon
07:16:01:             OS: Linux 5.3.0-42-generic x86_64
07:16:01:        OS Arch: AMD64
07:16:01:           GPUs: 1
07:16:01:          GPU 0: Bus:11 Slot:0 Func:0 AMD:6 Navi 10 [Radeon RX 5600 OEM/5600 XT
07:16:01:                 / 5700/5700 XT]
07:16:01:           CUDA: Not detected: Failed to open dynamic library 'libcuda.so':
07:16:01:                 libcuda.so: cannot open shared object file: No such file or
07:16:01:                 directory
07:16:01:OpenCL Device 0: Platform:0 Device:0 Bus:NA Slot:NA Compute:1.1 Driver:19.2
07:16:01:***********************************************************************
07:16:01:<config>
07:16:01:  <!-- Network -->
07:16:01:  <proxy v=':8080'/>
07:16:01:
07:16:01:  <!-- Slot Control -->
07:16:01:  <power v='full'/>
07:16:01:
07:16:01:  <!-- User Information -->
07:16:01:  <passkey v='********************************'/>
07:16:01:  <team v='243320'/>
07:16:01:  <user v='VulkanLogic'/>
07:16:01:
07:16:01:  <!-- Folding Slots -->
07:16:01:  <slot id='0' type='CPU'/>
07:16:01:</config>
07:16:01:Trying to access database...
07:16:01:Successfully acquired database lock
07:16:01:Enabled folding slot 00: READY cpu:16
07:16:01:WU01:FS00:Starting
07:16:01:WARNING:WU01:FS00:Changed SMP threads from 15 to 16 this can cause some work units to fail
07:16:01:WARNING:WU01:FS00:AS lowered CPUs from 16 to 15
07:16:01:WU01:FS00:Removing old file './work/01/logfile_01-20200319-064348.txt'
07:16:01:WU01:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /home/anon/cores/cores.foldingathome.org/v7/lin/64bit/avx/Core_a7.fah/FahCore_a7 -dir 01 -suffix 01 -version 705 -lifeline 22968 -checkpoint 15 -np 15
07:16:01:WU01:FS00:Started FahCore on PID 23012
07:16:01:WU01:FS00:Core PID:23016
07:16:01:WU01:FS00:FahCore 0xa7 started
07:16:01:WU01:FS00:0xa7:*********************** Log Started 2020-03-19T07:16:01Z ***********************
07:16:01:WU01:FS00:0xa7:************************** Gromacs Folding@home Core ***************************
07:16:01:WU01:FS00:0xa7:       Type: 0xa7
07:16:01:WU01:FS00:0xa7:       Core: Gromacs
07:16:01:WU01:FS00:0xa7:       Args: -dir 01 -suffix 01 -version 705 -lifeline 23012 -checkpoint 15 -np
07:16:01:WU01:FS00:0xa7:             15
07:16:01:WU01:FS00:0xa7:************************************ CBang *************************************
07:16:01:WU01:FS00:0xa7:       Date: Nov 5 2019
07:16:01:WU01:FS00:0xa7:       Time: 06:06:57
07:16:01:WU01:FS00:0xa7:   Revision: 46c96f1aa8419571d83f3e63f9c99a0d602f6da9
07:16:01:WU01:FS00:0xa7:     Branch: master
07:16:01:WU01:FS00:0xa7:   Compiler: GNU 8.3.0
07:16:01:WU01:FS00:0xa7:    Options: -std=c++11 -O3 -funroll-loops -fno-pie -fPIC
07:16:01:WU01:FS00:0xa7:   Platform: linux2 4.19.0-5-amd64
07:16:01:WU01:FS00:0xa7:       Bits: 64
07:16:01:WU01:FS00:0xa7:       Mode: Release
07:16:01:WU01:FS00:0xa7:************************************ System ************************************
07:16:01:WU01:FS00:0xa7:        CPU: AMD Ryzen 7 3700X 8-Core Processor
07:16:01:WU01:FS00:0xa7:     CPU ID: AuthenticAMD Family 23 Model 113 Stepping 0
07:16:01:WU01:FS00:0xa7:       CPUs: 16
07:16:01:WU01:FS00:0xa7:     Memory: 31.37GiB
07:16:01:WU01:FS00:0xa7:Free Memory: 1.13GiB
07:16:01:WU01:FS00:0xa7:    Threads: POSIX_THREADS
07:16:01:WU01:FS00:0xa7: OS Version: 5.3
07:16:01:WU01:FS00:0xa7:Has Battery: false
07:16:01:WU01:FS00:0xa7: On Battery: false
07:16:01:WU01:FS00:0xa7: UTC Offset: 1
07:16:01:WU01:FS00:0xa7:        PID: 23016
07:16:01:WU01:FS00:0xa7:        CWD: /home/anon/work
07:16:01:WU01:FS00:0xa7:******************************** Build - libFAH ********************************
07:16:01:WU01:FS00:0xa7:    Version: 0.0.18
07:16:01:WU01:FS00:0xa7:     Author: Joseph Coffland <joseph@cauldrondevelopment.com>
07:16:01:WU01:FS00:0xa7:  Copyright: 2019 foldingathome.org
07:16:01:WU01:FS00:0xa7:   Homepage: https://foldingathome.org/
07:16:01:WU01:FS00:0xa7:       Date: Nov 5 2019
07:16:01:WU01:FS00:0xa7:       Time: 06:13:26
07:16:01:WU01:FS00:0xa7:   Revision: 490c9aa2957b725af319379424d5c5cb36efb656
07:16:01:WU01:FS00:0xa7:     Branch: master
07:16:01:WU01:FS00:0xa7:   Compiler: GNU 8.3.0
07:16:01:WU01:FS00:0xa7:    Options: -std=c++11 -O3 -funroll-loops -fno-pie
07:16:01:WU01:FS00:0xa7:   Platform: linux2 4.19.0-5-amd64
07:16:01:WU01:FS00:0xa7:       Bits: 64
07:16:01:WU01:FS00:0xa7:       Mode: Release
07:16:01:WU01:FS00:0xa7:************************************ Build *************************************
07:16:01:WU01:FS00:0xa7:       SIMD: avx_256
07:16:01:WU01:FS00:0xa7:********************************************************************************
07:16:01:WU01:FS00:0xa7:Project: 13860 (Run 0, Clone 3921, Gen 0)
07:16:01:WU01:FS00:0xa7:Unit: 0x000000000d5a98395e725d67f03a15af
07:16:01:WU01:FS00:0xa7:Reading tar file core.xml
07:16:01:WU01:FS00:0xa7:Reading tar file frame0.tpr
07:16:01:WU01:FS00:0xa7:Digital signatures verified
07:16:01:WU01:FS00:0xa7:Calling: mdrun -s frame0.tpr -o frame0.trr -x frame0.xtc -e frame0.edr -cpt 15 -nt 15
07:16:01:WU01:FS00:0xa7:ERROR:
07:16:01:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
07:16:01:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
07:16:01:WU01:FS00:0xa7:ERROR:Source code file: /host/debian-stable-64bit-core-a7-avx-release/gromacs-core/build/gromacs/src/gromacs/fileio/gmxfio_xdr.c, line: 283
07:16:01:WU01:FS00:0xa7:ERROR:
07:16:01:WU01:FS00:0xa7:ERROR:Fatal error:
07:16:01:WU01:FS00:0xa7:ERROR:wrong string length 0 for string buf (source /host/debian-stable-64bit-core-a7-avx-release/gromacs-core/build/gromacs/src/gromacs/fileio/tpxio.c, line 3206)
07:16:01:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
07:16:01:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
07:16:01:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
07:16:06:WU01:FS00:0xa7:ERROR:
07:16:06:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
07:16:06:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
07:16:06:WU01:FS00:0xa7:ERROR:Source code file: /host/debian-stable-64bit-core-a7-avx-release/gromacs-core/build/gromacs/src/gromacs/fileio/tpxio.c, line: 3209
07:16:06:WU01:FS00:0xa7:ERROR:
07:16:06:WU01:FS00:0xa7:ERROR:Fatal error:
07:16:06:WU01:FS00:0xa7:ERROR:Can not read file frame0.tpr,
07:16:06:WU01:FS00:0xa7:ERROR:             this file is from a Gromacs version which is older than 2.0
07:16:06:WU01:FS00:0xa7:ERROR:             Make a new one with grompp or use a gro or pdb file, if possible
07:16:06:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
07:16:06:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
07:16:06:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
07:16:11:WU01:FS00:0xa7:ERROR:
07:16:11:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
07:16:11:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
07:16:11:WU01:FS00:0xa7:ERROR:Source code file: /host/debian-stable-64bit-core-a7-avx-release/gromacs-core/build/gromacs/src/gromacs/fileio/tpxio.c, line: 3218
07:16:11:WU01:FS00:0xa7:ERROR:
07:16:11:WU01:FS00:0xa7:ERROR:Fatal error:
07:16:11:WU01:FS00:0xa7:ERROR:Unknown precision in file frame0.tpr: real is 549316104 bytes instead of 4 or 8
07:16:11:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
07:16:11:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
07:16:11:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
07:16:16:WU01:FS00:0xa7:ERROR:
07:16:16:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
07:16:16:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
07:16:16:WU01:FS00:0xa7:ERROR:Source code file: /host/debian-stable-64bit-core-a7-avx-release/gromacs-core/build/gromacs/src/gromacs/fileio/gmxfio_xdr.c, line: 283
07:16:16:WU01:FS00:0xa7:ERROR:
07:16:16:WU01:FS00:0xa7:ERROR:Fatal error:
07:16:16:WU01:FS00:0xa7:ERROR:wrong string length 0 for string file_tag (source /host/debian-stable-64bit-core-a7-avx-release/gromacs-core/build/gromacs/src/gromacs/fileio/tpxio.c, line 3261)
07:16:16:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
07:16:16:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
07:16:16:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
07:16:21:WU01:FS00:0xa7:ERROR:
07:16:21:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
07:16:21:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
07:16:21:WU01:FS00:0xa7:ERROR:Source code file: /host/debian-stable-64bit-core-a7-avx-release/gromacs-core/build/gromacs/src/gromacs/fileio/tpxio.c, line: 3303
07:16:21:WU01:FS00:0xa7:ERROR:
07:16:21:WU01:FS00:0xa7:ERROR:Fatal error:
07:16:21:WU01:FS00:0xa7:ERROR:reading tpx file (frame0.tpr) version 549316480 with version 100 program
07:16:21:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
07:16:21:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
07:16:21:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
07:16:26:WU01:FS00:0xa7:WARNING:Unexpected exit() call
07:16:26:WU01:FS00:0xa7:WARNING:Unexpected exit from science code
07:16:26:WU01:FS00:0xa7:Saving result file ../logfile_01.txt
07:16:26:WU01:FS00:0xa7:Saving result file md.log
07:16:26:WU01:FS00:0xa7:Saving result file science.log
07:16:26:WU01:FS00:0xa7:Folding@home Core Shutdown: BAD_WORK_UNIT
07:16:27:WU01:FS00:FahCore returned: INTERRUPTED (102 = 0x66)

[Joe_H]

I have reported this to the person running this project.

[VulkanLogic]

Thanks.

Is there a way i can ditch this workitem and get a new one?

[Joe_H]

Did it not exit and return the WU as Faulty later on past the section of log you posted? Then Pause the folding, and it looks like you have placed the work files in /home/anon/work, remove a folder named '01', and then restart the folding. The client will detect the missing work files, and go to get another WU.

[VulkanLogic]

No, it did not exit and return the WU.
Thanks, manual removal worked.

[folder84]

Hi all. I just joined folding with some "spare resources". Also having a problem with this WU, and wanted to ask if this is related to me having too many CPU-s or possibly hitting the same error as VulkanLogic?

09:24:03:WU00:FS00:0xa7:ERROR:Fatal error:
09:24:03:WU00:FS00:0xa7:ERROR:There is no domain decomposition for 288 ranks that is compatible with the given box and a minimum cell size of 1.37225 nm

complete relevant infos:

Code: Select all

09:23:59:WU00:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /var/lib/fahclient/cores/cores.foldi
ngathome.org/v7/lin/64bit/avx/Core_a7.fah/FahCore_a7 -dir 00 -suffix 01 -version 705 -lifeline 1
 -checkpoint 15 -np 384
09:23:59:WU00:FS00:Started FahCore on PID 69747
09:23:59:Started thread 189 on PID 1
09:23:59:WU00:FS00:Core PID:69751
09:23:59:WU00:FS00:FahCore 0xa7 started
09:24:00:WU00:FS00:0xa7:*********************** Log Started 2020-03-19T09:23:59Z ***************
********
09:24:00:WU00:FS00:0xa7:************************** Gromacs Folding@home Core *******************
********
09:24:00:WU00:FS00:0xa7:       Type: 0xa7
09:24:00:WU00:FS00:0xa7:       Core: Gromacs
09:24:00:WU00:FS00:0xa7:       Args: -dir 00 -suffix 01 -version 705 -lifeline 69747 -checkpoint
 15 -np
09:24:00:WU00:FS00:0xa7:             384
09:24:00:WU00:FS00:0xa7:************************************ CBang *****************************
********
09:24:00:WU00:FS00:0xa7:       Date: Nov 5 2019
09:24:00:WU00:FS00:0xa7:       Time: 06:06:57
09:24:00:WU00:FS00:0xa7:   Revision: 46c96f1aa8419571d83f3e63f9c99a0d602f6da9
09:24:00:WU00:FS00:0xa7:     Branch: master
09:24:00:WU00:FS00:0xa7:   Compiler: GNU 8.3.0
09:24:00:WU00:FS00:0xa7:    Options: -std=c++11 -O3 -funroll-loops -fno-pie -fPIC
09:24:00:WU00:FS00:0xa7:   Platform: linux2 4.19.0-5-amd64
09:24:00:WU00:FS00:0xa7:       Bits: 64
09:24:00:WU00:FS00:0xa7:       Mode: Release
09:24:00:WU00:FS00:0xa7:************************************ System ****************************
********
09:24:00:WU00:FS00:0xa7:        CPU: Intel(R) Xeon(R) Platinum 8160 CPU @ 2.10GHz
09:24:00:WU00:FS00:0xa7:     CPU ID: GenuineIntel Family 6 Model 85 Stepping 4
09:24:00:WU00:FS00:0xa7:       CPUs: 384
09:24:00:WU00:FS00:0xa7:     Memory: 1006.51GiB
09:24:00:WU00:FS00:0xa7:Free Memory: 979.21GiB
09:24:00:WU00:FS00:0xa7:    Threads: POSIX_THREADS
09:24:00:WU00:FS00:0xa7: OS Version: 4.4
09:24:00:WU00:FS00:0xa7:Has Battery: false
09:24:00:WU00:FS00:0xa7: On Battery: false
09:24:00:WU00:FS00:0xa7: UTC Offset: 0
09:24:00:WU00:FS00:0xa7:        PID: 69751
09:24:00:WU00:FS00:0xa7:        CWD: /var/lib/fahclient/work
09:24:00:WU00:FS00:0xa7:******************************** Build - libFAH ************************
********
09:24:00:WU00:FS00:0xa7:    Version: 0.0.18
09:24:00:WU00:FS00:0xa7:     Author: Joseph Coffland <joseph@cauldrondevelopment.com>
09:24:00:WU00:FS00:0xa7:  Copyright: 2019 foldingathome.org
09:24:00:WU00:FS00:0xa7:   Homepage: https://foldingathome.org/
09:24:00:WU00:FS00:0xa7:       Date: Nov 5 2019
09:24:00:WU00:FS00:0xa7:       Time: 06:13:26
09:24:00:WU00:FS00:0xa7:   Revision: 490c9aa2957b725af319379424d5c5cb36efb656
09:24:00:WU00:FS00:0xa7:     Branch: master
09:24:00:WU00:FS00:0xa7:   Compiler: GNU 8.3.0
09:24:00:WU00:FS00:0xa7:    Options: -std=c++11 -O3 -funroll-loops -fno-pie
09:24:00:WU00:FS00:0xa7:   Platform: linux2 4.19.0-5-amd64
09:24:00:WU00:FS00:0xa7:       Bits: 64
09:24:00:WU00:FS00:0xa7:       Mode: Release
09:24:00:WU00:FS00:0xa7:************************************ Build *****************************
********
09:24:00:WU00:FS00:0xa7:       SIMD: avx_256
09:24:00:WU00:FS00:0xa7:************************************************************************
********
09:24:00:WU00:FS00:0xa7:Project: 13860 (Run 0, Clone 15190, Gen 0)
09:24:00:WU00:FS00:0xa7:Unit: 0x000000000d5a98395e73109f9c2fc0c1
09:24:00:WU00:FS00:0xa7:Reading tar file core.xml
09:24:00:WU00:FS00:0xa7:Reading tar file frame0.tpr
09:24:00:WU00:FS00:0xa7:Digital signatures verified
09:24:00:WU00:FS00:0xa7:Calling: mdrun -s frame0.tpr -o frame0.trr -x frame0.xtc -e frame0.edr -
cpt 15 -nt 384
09:24:01:Server connection id=1 on 0.0.0.0:36330 from 127.0.0.1
09:24:01:Started thread 190 on PID 1
09:24:01:FS00:Paused
09:24:01:FS00:Shutting core down
09:24:01:WU00:FS00:0xa7:Caught signal SIGINT(2) on PID 69751
09:24:01:WU00:FS00:0xa7:Exiting, please wait. . .
09:24:02:Server connection id=1 ended
09:24:03:WU00:FS00:0xa7:Steps: first=0 total=125000
09:24:03:WU00:FS00:0xa7:ERROR:
09:24:03:WU00:FS00:0xa7:ERROR:-------------------------------------------------------
09:24:03:WU00:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
09:24:03:WU00:FS00:0xa7:ERROR:Source code file: /host/debian-stable-64bit-core-a7-avx-release/gr
omacs-core/build/gromacs/src/gromacs/mdlib/domdec.c, line: 6902
09:24:03:WU00:FS00:0xa7:ERROR:
09:24:03:WU00:FS00:0xa7:ERROR:Fatal error:
09:24:03:WU00:FS00:0xa7:ERROR:There is no domain decomposition for 288 ranks that is compatible
with the given box and a minimum cell size of 1.37225 nm
09:24:03:WU00:FS00:0xa7:ERROR:Change the number of ranks or mdrun option -rcon or -dds or your L
INCS settings
09:24:03:WU00:FS00:0xa7:ERROR:Look in the log file for details on the domain decomposition
09:24:03:WU00:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check th
e GROMACS
09:24:03:WU00:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
09:24:03:WU00:FS00:0xa7:ERROR:-------------------------------------------------------
09:24:09:WU00:FS00:0xa7:WARNING:Unexpected exit() call
09:24:09:WU00:FS00:0xa7:WARNING:Unexpected exit from science code

[Joe_H]

Yes, that would be from too many CPU threads.

Some of the recent projects have been pushed out quickly, and tests for the maximum number of threads they can run on may not have been completed. So restrictions may not have been put in place completely. If you still have this WU, or similar and are willing to test what counts work, you can post that here and we can get that information back to the researchers.

You would need to pause the folding, change the thread count in FAHControl, and resume after saving the change. I do know on large enough protein systems the folding core can handle many threads, tests have been done over 200. Counts that can be used are multiples of 2, 3, and sometimes 5. Multiples of prime numbers 7 and greater can not.