running error on Calab

[smazrouee]

Sounds like problem with docker deamon or sth

FAVITES Version

Environment

Configuration File

{
"ContactNetwork": "NetworkX",
"ContactNetworkGenerator": "RandomPartitionGraph",
"d_or_u": "u",

"rpg_p_in": 0.004,
"rpg_p_out": 0.0002,
"rpg_sizes": [1000,1000,1000,1000,1000],
"end_time": 10,
"num_seeds": 50,
"out_dir": "/Users/sepideh/FAVITES/output/set1/output_1_1",

"Driver": "Default",
"EndCriteria": "GEMF",
"Logging": "File",

"NodeAvailability": "Bernoulli",
"node_sample_prob": 0.1,
"NumBranchSample": "Single",
"NumTimeSample": "Once",
"SourceSample": "Random",
"TimeSample": "GranichFirstART",

"NodeEvolution": "VirusTreeSimulator",
"vts_growthRate": 2.851904,
"vts_model": "logistic",
"vts_n0": 1,
"vts_t50": -2,

"PostValidation": "Dummy",

"SeedSelection": "Random",

"SeedSequence": "VirusPureCoalescentGTRGamma",
"viral_sequence_type": "HIV1-B-DNA-POL-LITTLE",

"SequenceEvolution": "GTRGammaSeqGen",
"Sequencing": "Perfect",

"TransmissionNodeSample": "GEMF",
"hiv_a1_to_d": 0,
"hiv_a2_to_a3": 0,
"hiv_a2_to_d": 0,
"hiv_a1_to_i1": 0.48,
"hiv_a2_to_i2": 0.48,
"hiv_i2_to_a2": 0.5,
"hiv_i1_to_a1": 0.5,
"hiv_a3_to_a4": 0,
"hiv_a3_to_d": 0,
"hiv_a3_to_i3": 0,
"hiv_a4_to_d": 0,
"hiv_a4_to_i4": 0,
"hiv_i1_to_d": 0,
"hiv_i1_to_i2": 8.666666666666666,
"hiv_a1_to_a2": 4.33333,
"hiv_i2_to_d": 0,
"hiv_i2_to_i3": 0,
"hiv_i3_to_a3": 0,
"hiv_i3_to_d": 0,
"hiv_i3_to_i4": 0,
"hiv_i4_to_a4": 0,
"hiv_i4_to_d": 0,
"hiv_ns_to_d": 0,
"hiv_ns_to_s": 999999,
"hiv_s_to_d": 0,
"hiv_s_to_i1_by_a1": 0.005625,
"hiv_s_to_i1_by_a2": 0,
"hiv_s_to_i1_by_a3": 0,
"hiv_s_to_i1_by_a4": 0,
"hiv_s_to_i1_by_i1": 0.1125,
"hiv_s_to_i1_by_i2": 0.1,
"hiv_s_to_i1_by_i3": 0,
"hiv_s_to_i1_by_i4": 0,
"hiv_s_to_i1_seed": 0,
"TransmissionTimeSample": "HIVARTGranichGEMF",

"TreeNode": "Simple",
"TreeUnit": "LogNormal",
"tree_rate_mean": -6.164,
"tree_rate_stdev": 0.3,

"grinder_path": "grinder",
"gemf_path": "GEMF",
"hmmemit_path": "hmmemit",
"java_path": "java",
"nw_rename_path": "nw_rename",
"seqgen_path": "seq-gen",

"seed_population": 20,

"seqgen_a_to_c": 1.765707,
"seqgen_a_to_g": 9.587649,
"seqgen_a_to_t": 0.691915,
"seqgen_c_to_g": 0.863348,
"seqgen_c_to_t": 10.282617,
"seqgen_freq_a": 0.392,
"seqgen_freq_c": 0.165,
"seqgen_freq_g": 0.212,
"seqgen_freq_t": 0.232,
"seqgen_g_to_t": 1.0,
"seqgen_gamma_shape": 0.405129,
"seqgen_num_gamma_rate_categories": ""

}

Unexpected Behavior

run_favites_docker.py -c CONFIG1-1.json
Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Get http://%2Fvar%2Frun%2Fdocker.sock/v1.35/images/json: dial unix /var/run/docker.sock: connect: permission denied
Traceback (most recent call last):
File "/calab_data/mirarab/home//sepideh/.bin/run_favites_docker.py", line 31, in
o = check_output(['docker','images']).decode().splitlines()
File "/usr/lib/python3.4/subprocess.py", line 620, in check_output
raise CalledProcessError(retcode, process.args, output=output)
subprocess.CalledProcessError: Command '['docker', 'images']' returned non-zero exit status 1

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/calab_data/mirarab/home//sepideh/.bin/run_favites_docker.py", line 36, in
raise RuntimeError("docker images command failed\n%s"%e.output)
RuntimeError: docker images command failed
b''

[niemasd]

The issue is your output directory. You're specifying a directory that's in root. You should specify output directories you have write access to. For example, this worked for me:

~/bin/FAVITES/run_favites_docker.py -c test.json -o test

where test.json is the config file you list here

[niemasd]

Actually, looking at this, your error was when my script tried to run the docker images command, which is strange because I just ran it fine right now on Calab

[niemasd]

I'm able to consistently run docker images and whatnot on Calab, so I'm going to close this

[smazrouee]

Update for future references: the problem is resolved for my user today, when Calab admin granted my user credentials to run docker without sudo access (sudo usermod -a -G docker [username]). Before then I was getting RuntimeError: docker images command failed. Let's not rush to closing an issue before it's fixed for other users. Your username is good for testing but probably not the best indication of resolving the problem if you don't see any errors.

…

On Tue, Mar 13, 2018 at 4:58 PM, Niema Moshiri ***@***.***> wrote: I'm able to consistently run docker images and whatnot on Calab, so I'm going to close this — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#6 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFgEEE6gJbi9wYL4Qoeg_moUomcdWvXXks5teF0ngaJpZM4So_Rc> .