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Linux versions of GARLI temporarily deprecated
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Message boards : News : Linux versions of GARLI temporarily deprecated

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Profile Adam Bazinet
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Message 6354 - Posted: 3 Aug 2015, 18:38:25 UTC

I have had to temporarily deactivate our Linux versions of GARLI due to a bug preventing all workunits from completing properly under our new phased workunit scheme. Hopefully this bug will be resolved relatively soon; in the meantime, my apologies to our Linux users.

Profile Bryan
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Message 6355 - Posted: 3 Aug 2015, 19:54:20 UTC - in response to Message 6354.

So does that indicate that there is work available for Windows?

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Message 6372 - Posted: 21 Sep 2015, 18:40:59 UTC

Is linux application still disabled?

Thanks

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Message 6403 - Posted: 26 Oct 2015, 11:13:33 UTC - in response to Message 6372.

Is linux application still disabled?

Thanks


I did not see an answer for this, Is the Linux application still not working?

Thanks
Conan
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BobCat13
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Message 6423 - Posted: 9 Nov 2015, 23:14:35 UTC - in response to Message 6354.

I have had to temporarily deactivate our Linux versions of GARLI due to a bug preventing all workunits from completing properly under our new phased workunit scheme. Hopefully this bug will be resolved relatively soon; in the meantime, my apologies to our Linux users.

I may have found something for you to investiage, Adam. When the server assigns tasks to my 64-bit Linux machine, the _initial and _main tasks use the 64-bit science app. When it assigns the _final tasks, it uses the 32-bit app. I noticed all of the other users who have failures on the _final tasks are also being assigned the 32-bit app. On the most recent _final task, I stopped the client, edited the client_state.xml and changed the result to use the 64-bit app and it completed and validated.

Link to a 32-bit _final task:
http://boinc.umiacs.umd.edu/result.php?resultid=5838654

Link to the edited to use 64-bit _final task:
http://boinc.umiacs.umd.edu/result.php?resultid=5841776

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Message 6505 - Posted: 16 Feb 2016, 20:23:45 UTC - in response to Message 6423.

Here is another problem. The server is mixing architectures on Linux when sending out the next step on these divided tasks. I received one for 64-bit when the previous step had been run on 32-bit architecture. The 64-bit try caused an error within 2 seconds of starting, with the following in the _5 output file (notice the blue text I have highlighted):

    Running BOINC GARLI Version 2.1.1129 (10 Sep 2014)
    ->Single processor version for 32-bit OS<-
    ##############################################################
    This is GARLI 2.1: maximum likelihood phylogenetic inference
    using nucleotide, amino acid, codon and morphology-like data,
    as well as partitioned models.
    General program usage is extensively documented here:
    http://www.nescent.org/wg/garli/
    See this page for details on partitioned model usage:
    http://www.nescent.org/wg_garli/Using_partitioned_models
    and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
    PLEASE LET ME KNOW OF ANY PROBLEMS AT:
    garli.support@gmail.com
    ##############################################################
    Compiled Oct 3 2014 13:48:23 using GNU gcc compiler version 4.1.2
    Using NCL version 2.1.17

    #######################################################
    Reading config file garli.conf
    ###################################################
    READING OF DATA
    Attempting to read data file in Nexus format (using NCL):
    EriolaenaCOMB1.0data.nex ...
    Reading DATA block... successful

    ###################################################
    PARTITIONING OF DATA AND MODELS
    GARLI data subset 1
    CHARACTERS block #1 ("Untitled DATA Block 1")
    Data read as Nucleotide data,
    modeled as Nucleotide data
    Summary of data:
    167 sequences.
    4876 constant characters.
    532 parsimony-informative characters.
    593 uninformative variable characters.
    11 characters were completely missing or ambiguous (removed).
    6001 total characters (6012 before removing empty columns).
    2174 unique patterns in compressed data matrix.

    ###################################################
    NOTE: Unlike many programs, the amount of system memory that Garli will
    use can be controlled by the user.
    (This comes from the availablememory setting in the configuration file.
    Availablememory should NOT be set to more than the actual amount of
    physical memory that your computer has installed)

    For this dataset:
    Mem level availablememory setting
    great >= 452 MB
    good approx 452 MB to 285 MB
    low approx 284 MB to 116 MB
    very low approx 115 MB to 88 MB
    the minimum required availablememory is 88 MB

    You specified that Garli should use at most 452.0 MB of memory.

    Garli will actually use approx. 451.9 MB of memory
  • *Your memory level is: great (you don't need to change anything)**

    #######################################################
    STARTING RUN
    MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
    Model 1
    Number of states = 4 (nucleotide data)
    Nucleotide Relative Rate Matrix: 6 rates
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
    Equilibrium State Frequencies: estimated
    (ACGT) 0.3115 0.1845 0.1853 0.3187
    Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
    0.5000
    with an invariant (invariable) site category, proportion estimated
    0.2031
    Substitution rate categories under this model:
    rate proportion
    0.0000 0.2031
    0.0334 0.1992
    0.2519 0.1992
    0.8203 0.1992
    2.8944 0.1992

    Starting with seed=913492

    creating likelihood stepwise addition starting tree...
    number of taxa added:
    4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84
    Optimizing parameters... improved 159.222 lnL
    Optimizing branchlengths... improved 37.157 lnL
    85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167
    Initial ln Likelihood: -23741.7484
    optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs...
    pass 1:+ 185.219 (branch= 55.30 scale= 9.83 alpha= 4.66 freqs= 4.51 rel rates=110.91 pinv= 0.00)
    pass 2:+ 83.407 (branch= 20.33 scale= 0.56 alpha= 1.66 freqs= 5.87 rel rates= 9.54 pinv= 45.45)
    pass 3:+ 70.102 (branch= 12.59 scale= 0.56 alpha= 34.66 freqs= 0.17 rel rates= 0.72 pinv= 21.41)
    pass 4:+ 30.773 (branch= 0.43 scale= 0.00 alpha= 18.74 freqs= 0.13 rel rates= 0.01 pinv= 11.47)
    pass 5:+ 16.078 (branch= 0.89 scale= 0.00 alpha= 9.08 freqs= 0.08 rel rates= 0.01 pinv= 6.01)
    pass 6:+ 6.580 (branch= 0.00 scale= 0.00 alpha= 5.40 freqs= 0.04 rel rates= 0.01 pinv= 1.13)
    pass 7:+ 3.136 (branch= 0.00 scale= 0.00 alpha= 2.25 freqs= 0.01 rel rates= 0.01 pinv= 0.87)
    pass 8:+ 1.131 (branch= 0.00 scale= 0.00 alpha= 1.08 freqs= 0.01 rel rates= 0.01 pinv= 0.04)
    pass 9:+ 0.049 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.00 rel rates= 0.01 pinv= 0.04)
    lnL after optimization: -23345.2746

    NOTE: Terminating run after initial optimization and writing
    checkpoint because workphasedivision configuration entry was set.

    Running BOINC GARLI Version 2.1.1129 (10 Sep 2014)
    Found BOINC checkpoint files. Restarting....

    ->Single processor version for 64-bit OS<-
    ##############################################################
    This is GARLI 2.1: maximum likelihood phylogenetic inference
    using nucleotide, amino acid, codon and morphology-like data,
    as well as partitioned models.
    General program usage is extensively documented here:
    http://www.nescent.org/wg/garli/
    See this page for details on partitioned model usage:
    http://www.nescent.org/wg_garli/Using_partitioned_models
    and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
    PLEASE LET ME KNOW OF ANY PROBLEMS AT:
    garli.support@gmail.com
    ##############################################################
    Compiled Oct 6 2014 13:23:56 using GNU gcc compiler version 4.1.2
    Using NCL version 2.1.17

    #######################################################
    Reading config file garli.conf
    ###################################################
    READING OF DATA
    Attempting to read data file in Nexus format (using NCL):
    EriolaenaCOMB1.0data.nex ...
    Reading DATA block... successful

    ###################################################
    PARTITIONING OF DATA AND MODELS
    GARLI data subset 1
    CHARACTERS block #1 ("Untitled DATA Block 1")
    Data read as Nucleotide data,
    modeled as Nucleotide data
    Summary of data:
    167 sequences.
    4876 constant characters.
    532 parsimony-informative characters.
    593 uninformative variable characters.
    11 characters were completely missing or ambiguous (removed).
    6001 total characters (6012 before removing empty columns).
    2174 unique patterns in compressed data matrix.

    ###################################################
    NOTE: Unlike many programs, the amount of system memory that Garli will
    use can be controlled by the user.
    (This comes from the availablememory setting in the configuration file.
    Availablememory should NOT be set to more than the actual amount of
    physical memory that your computer has installed)

    For this dataset:
    Mem level availablememory setting
    great >= 452 MB
    good approx 452 MB to 285 MB
    low approx 284 MB to 116 MB
    very low approx 115 MB to 88 MB
    the minimum required availablememory is 88 MB

    You specified that Garli should use at most 452.0 MB of memory.

    Garli will actually use approx. 451.9 MB of memory
  • *Your memory level is: great (you don't need to change anything)**

    #######################################################
    STARTING RUN

    ERROR: State frequencies do not appear to add up to 1.0!



I edited the client_state file to change the architecture to 32-bit, corrected the necessary entries to mark the task as new, and started the client again. It ran correctly as a 32-bit task on machine 114545, linked here.

Either the system needs to mark these tasks for the correct architecture based upon the previous step, or you could depreciate the 32-bit linux app as according to the Applications page it only has 1 GigaFLOPS average computing power anyway.

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Message 6506 - Posted: 16 Feb 2016, 20:28:33 UTC - in response to Message 6505.

Follow up post, using the _5 output file created by running the 32-bit application successfully:

    Running BOINC GARLI Version 2.1.1129 (10 Sep 2014)
    ->Single processor version for 32-bit OS<-
    ##############################################################
    This is GARLI 2.1: maximum likelihood phylogenetic inference
    using nucleotide, amino acid, codon and morphology-like data,
    as well as partitioned models.
    General program usage is extensively documented here:
    http://www.nescent.org/wg/garli/
    See this page for details on partitioned model usage:
    http://www.nescent.org/wg_garli/Using_partitioned_models
    and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
    PLEASE LET ME KNOW OF ANY PROBLEMS AT:
    garli.support@gmail.com
    ##############################################################
    Compiled Oct 3 2014 13:48:23 using GNU gcc compiler version 4.1.2
    Using NCL version 2.1.17

    #######################################################
    Reading config file garli.conf
    ###################################################
    READING OF DATA
    Attempting to read data file in Nexus format (using NCL):
    EriolaenaCOMB1.0data.nex ...
    Reading DATA block... successful

    ###################################################
    PARTITIONING OF DATA AND MODELS
    GARLI data subset 1
    CHARACTERS block #1 ("Untitled DATA Block 1")
    Data read as Nucleotide data,
    modeled as Nucleotide data
    Summary of data:
    167 sequences.
    4876 constant characters.
    532 parsimony-informative characters.
    593 uninformative variable characters.
    11 characters were completely missing or ambiguous (removed).
    6001 total characters (6012 before removing empty columns).
    2174 unique patterns in compressed data matrix.

    ###################################################
    NOTE: Unlike many programs, the amount of system memory that Garli will
    use can be controlled by the user.
    (This comes from the availablememory setting in the configuration file.
    Availablememory should NOT be set to more than the actual amount of
    physical memory that your computer has installed)

    For this dataset:
    Mem level availablememory setting
    great >= 452 MB
    good approx 452 MB to 285 MB
    low approx 284 MB to 116 MB
    very low approx 115 MB to 88 MB
    the minimum required availablememory is 88 MB

    You specified that Garli should use at most 452.0 MB of memory.

    Garli will actually use approx. 451.9 MB of memory
  • *Your memory level is: great (you don't need to change anything)**

    #######################################################
    STARTING RUN
    MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
    Model 1
    Number of states = 4 (nucleotide data)
    Nucleotide Relative Rate Matrix: 6 rates
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
    Equilibrium State Frequencies: estimated
    (ACGT) 0.3115 0.1845 0.1853 0.3187
    Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
    0.5000
    with an invariant (invariable) site category, proportion estimated
    0.2031
    Substitution rate categories under this model:
    rate proportion
    0.0000 0.2031
    0.0334 0.1992
    0.2519 0.1992
    0.8203 0.1992
    2.8944 0.1992

    Starting with seed=913492

    creating likelihood stepwise addition starting tree...
    number of taxa added:
    4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84
    Optimizing parameters... improved 159.222 lnL
    Optimizing branchlengths... improved 37.157 lnL
    85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167
    Initial ln Likelihood: -23741.7484
    optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs...
    pass 1:+ 185.219 (branch= 55.30 scale= 9.83 alpha= 4.66 freqs= 4.51 rel rates=110.91 pinv= 0.00)
    pass 2:+ 83.407 (branch= 20.33 scale= 0.56 alpha= 1.66 freqs= 5.87 rel rates= 9.54 pinv= 45.45)
    pass 3:+ 70.102 (branch= 12.59 scale= 0.56 alpha= 34.66 freqs= 0.17 rel rates= 0.72 pinv= 21.41)
    pass 4:+ 30.773 (branch= 0.43 scale= 0.00 alpha= 18.74 freqs= 0.13 rel rates= 0.01 pinv= 11.47)
    pass 5:+ 16.078 (branch= 0.89 scale= 0.00 alpha= 9.08 freqs= 0.08 rel rates= 0.01 pinv= 6.01)
    pass 6:+ 6.580 (branch= 0.00 scale= 0.00 alpha= 5.40 freqs= 0.04 rel rates= 0.01 pinv= 1.13)
    pass 7:+ 3.136 (branch= 0.00 scale= 0.00 alpha= 2.25 freqs= 0.01 rel rates= 0.01 pinv= 0.87)
    pass 8:+ 1.131 (branch= 0.00 scale= 0.00 alpha= 1.08 freqs= 0.01 rel rates= 0.01 pinv= 0.04)
    pass 9:+ 0.049 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.00 rel rates= 0.01 pinv= 0.04)
    lnL after optimization: -23345.2746

    NOTE: Terminating run after initial optimization and writing
    checkpoint because workphasedivision configuration entry was set.

    Running BOINC GARLI Version 2.1.1129 (10 Sep 2014)
    Found BOINC checkpoint files. Restarting....

    ->Single processor version for 32-bit OS<-
    ##############################################################
    This is GARLI 2.1: maximum likelihood phylogenetic inference
    using nucleotide, amino acid, codon and morphology-like data,
    as well as partitioned models.
    General program usage is extensively documented here:
    http://www.nescent.org/wg/garli/
    See this page for details on partitioned model usage:
    http://www.nescent.org/wg_garli/Using_partitioned_models
    and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
    PLEASE LET ME KNOW OF ANY PROBLEMS AT:
    garli.support@gmail.com
    ##############################################################
    Compiled Oct 3 2014 13:48:23 using GNU gcc compiler version 4.1.2
    Using NCL version 2.1.17

    #######################################################
    Reading config file garli.conf
    ###################################################
    READING OF DATA
    Attempting to read data file in Nexus format (using NCL):
    EriolaenaCOMB1.0data.nex ...
    Reading DATA block... successful

    ###################################################
    PARTITIONING OF DATA AND MODELS
    GARLI data subset 1
    CHARACTERS block #1 ("Untitled DATA Block 1")
    Data read as Nucleotide data,
    modeled as Nucleotide data
    Summary of data:
    167 sequences.
    4876 constant characters.
    532 parsimony-informative characters.
    593 uninformative variable characters.
    11 characters were completely missing or ambiguous (removed).
    6001 total characters (6012 before removing empty columns).
    2174 unique patterns in compressed data matrix.

    ###################################################
    NOTE: Unlike many programs, the amount of system memory that Garli will
    use can be controlled by the user.
    (This comes from the availablememory setting in the configuration file.
    Availablememory should NOT be set to more than the actual amount of
    physical memory that your computer has installed)

    For this dataset:
    Mem level availablememory setting
    great >= 452 MB
    good approx 452 MB to 285 MB
    low approx 284 MB to 116 MB
    very low approx 115 MB to 88 MB
    the minimum required availablememory is 88 MB

    You specified that Garli should use at most 452.0 MB of memory.

    Garli will actually use approx. 451.9 MB of memory
  • *Your memory level is: great (you don't need to change anything)**

    #######################################################
    STARTING RUN

    Restarting from checkpoint...
    generation 0, seed 1151191669, best lnL -23345.275
    gen current_lnL precision last_tree_imp
    0 -23345.2746 0.500 0
    Optimization precision reduced
    Optimizing parameters... improved 0.004 lnL
    Optimizing branchlengths... improved 0.021 lnL
    Optimization precision reduced
    Optimizing parameters... improved 0.001 lnL
    Optimizing branchlengths... improved 0.000 lnL
    Optimization precision reduced
    Optimizing parameters... improved 0.001 lnL
    Optimizing branchlengths... improved 0.000 lnL
    Optimization precision reduced
    Optimizing parameters... improved 0.004 lnL
    Optimizing branchlengths... improved 0.000 lnL
    Optimization precision reduced
    Optimizing parameters... improved 0.007 lnL
    Optimizing branchlengths... improved 1.129 lnL
    Optimization precision reduced
    Optimizing parameters... improved 0.004 lnL
    Optimizing branchlengths... improved 0.667 lnL
    Optimization precision reduced
    Optimizing parameters... improved 0.001 lnL
    Optimizing branchlengths... improved 1.229 lnL
    Optimization precision reduced
    Optimizing parameters... improved 0.001 lnL
    Optimizing branchlengths... improved 1.631 lnL
    Optimization precision reduced
    Optimizing parameters... improved 0.001 lnL
    Optimizing branchlengths... improved 0.554 lnL
    Optimization precision reduced
    Optimizing parameters... improved 0.000 lnL
    Optimizing branchlengths... improved 0.304 lnL
    Optimizing parameters... improved 0.000 lnL
    Optimizing branchlengths... improved 0.252 lnL
    Optimizing parameters... improved 0.000 lnL
    Optimizing branchlengths... improved 0.000 lnL
    Optimizing parameters... improved 0.000 lnL
    Optimizing branchlengths... improved 0.000 lnL
    Optimizing parameters... improved 0.000 lnL
    Optimizing branchlengths... improved 0.000 lnL
    Optimizing parameters... improved 0.000 lnL
    Optimizing branchlengths... improved 0.000 lnL
    Optimizing parameters... improved 0.000 lnL
    Optimizing branchlengths... improved 0.000 lnL
    Optimizing parameters... improved 0.000 lnL
    Optimizing branchlengths... improved 0.000 lnL
    Optimizing parameters... improved 0.000 lnL
    Optimizing branchlengths... improved 0.000 lnL
    Optimizing parameters... improved 0.000 lnL
    Optimizing branchlengths... improved 0.000 lnL
    Reached termination condition!
    last topological improvement at gen 56043
    Improvement over last 500 gen = 0.00011

    NOTE: Terminating run before final optimization and writing checkpoint
    because workphasedivision configuration entry was set.

BobCat13
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Message 6509 - Posted: 17 Feb 2016, 20:51:24 UTC - in response to Message 6506.
Last modified: 17 Feb 2016, 21:09:17 UTC

LOL, my Linux machine just received 7 tasks (4 32-bit and 3 64-bit) and everyone of them was assigned to the incorrect architecture when comparing the <result> in client_state to the _6 input file that corresponds to each task. I stopped the client and edited the client_state to correct the bad assignments, but that would be a bit much to expect from anyone running this project as their top priority project.

Edit: Received one more. Should be 32-bit, but was assigned to 64-bit.

BobCat13
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Message 6515 - Posted: 6 Mar 2016, 2:51:20 UTC - in response to Message 6509.

This is still happening. Just had to edit the client_state.xml because a divided task that had previously run as 64-bit was assigned to run as 32-bit on the next step.

I also checked the other Linux machines on that task and noticed an error rate that ranged from 20% to 83%. Since the 32-bit app is still showing just 1 GigaFLOPS, would it be possible to remove the 32-bit app and just keep the 64-bit app for Linux?

Profile [AF>EDLS]GuL
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Message 6561 - Posted: 24 Aug 2016, 18:23:52 UTC

Hi,
I am afraid the problem is back again : http://boinc.umiacs.umd.edu/result.php?resultid=8502939 . But it has worked on the same computer : http://boinc.umiacs.umd.edu/result.php?resultid=8297932 .

BobCat13, can you explain a little bit more what change you've done in client_state.xml ? Can we either use an app_config.xml ?

Thanks
____________

Mike
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Message 6562 - Posted: 29 Aug 2016, 11:55:39 UTC - in response to Message 6561.
Last modified: 29 Aug 2016, 12:01:48 UTC

I'm seeing problems here too, 64 bit Debian Stretch VM, running on an Illumos (SmartOS) hypervisor, BOINC client version 7.6.33.

Many work units erroring out immediately (1 (0x1) Unknown error number), many apparently completing but after a couple of seconds of CPU time. One[1] seemed to go on forever, but that seems to just be a broken WU, since other crunchers are struggling with it too.

Seemingly all started on the 24th.


[1] : http://boinc.umiacs.umd.edu/workunit.php?wuid=4257637

Engagex BOINC-SETI
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Message 6655 - Posted: 9 Mar 2017, 21:16:37 UTC

Does this have anything to do with it needing 12Gb ram?


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