trying to get this working on the cluster

[dpschreiner]

I am submitting this job on our cluster using slurm with:

models <- dynwrap::infer_trajectories(
  dataset, 
  method = list(ti_slingshot(), ti_mst(), ti_slice(), ti_pcreode())
)

and this is returned to me. is it normal for the protocol string for singularity to say docker?

STDOUT
Running singularity exec 'docker://dynverse/ti_slingshot:v1.0.3' echo hi

STDERR
Error in processx::run("singularity", c("exec", paste0("docker://", container_id),  : 
  System command error
Calls: <Anonymous> ... create_ti_method_container -> <Anonymous> -> <Anonymous>
Execution halted

$ singularity --version
singularity version 3.3.0-1.el7

[zouter]

Hmmm that's weird! You have the correct singularity version for sure. Could you try to run singularity exec 'docker://dynverse/ti_slingshot:v1.0.3' echo hi in the command line and see what that gives as output? It might be that some singularity syntax changed in recent releases...

[dpschreiner]

ah, OK. it seems to be working there. i think on the cluster there is no external internet access by default. will follow up with the admins - thanks!

[dpschreiner]

Hmmm that's weird! You have the correct singularity version for sure. Could you try to run singularity exec 'docker://dynverse/ti_slingshot:v1.0.3' echo hi in the command line and see what that gives as output? It might be that some singularity syntax changed in recent releases...

actually: where can i access the ti_* images so i can download them manually?

[zouter]

Alright, makes sense! If you run singularity exec 'docker://dynverse/ti_slingshot:v1.0.3' echo hi (as an example), singularity will store them inside .singularity. You can transfer these to the cluster and specify your singularity cache dir using:

config <- babelwhale::create_singularity_config(cache_dir = "YOUR SINGULARITY CACHE DIR")
babelwhale::set_default_config(config)

This should work, but happy to help further!

[dpschreiner]

OK, now i'm hitting this issue from babelwhale:

Error in save(config, file = config_file, compress = "gz") : 
  'compress = "gz"' is invalid

perhaps just setting compress = TRUE would be sufficient?

[dpschreiner]

OK, i set permanent=FALSE there and still it's not finding the containers. what should the cache_dir actually contain? in other issues i see some manual commands that refer to the .sif file. in my ~/.singularity i have:

$ find . -name '*sif'
./cache/oci-tmp/fc54a7a1b9f78f38dbf36e0acaf0ee74ef9eba56aa5a9a8c5702a8a8e34aa815/ti_slingshot_v1.0.3.sif
./cache/oci-tmp/4d1da3d4a0a4766fdb9feeef4c49bca5844df0d36259d2cb9a8d7fa9a9382539/ti_slice_v0.9.9.01.sif
./cache/oci-tmp/93dad934d965258a3968346b5bfe47266ce41330576c5d42bd5e9d61492e1ec3/ti_pcreode_v0.9.9.01.sif
./cache/oci-tmp/8421d9a84432575381bfabd248f1eb56f3aa21d9d7cd2511583c68c9b7511d10/alpine_3.7.sif
./cache/oci-tmp/24980c21366515cb2e16ce89cd167237ba867dd75513a95ed47185e9ca9d6f27/ti_mst_v0.9.9.01.sif

i.e. the sif files are all in oci-tmp. i tried symlinking to them from the cache dir, still didn't work. do i need a separate config setting for each sif? then i would have to loop through methods, which isn't a problem. here is what i'm running, where MY_HOME_DIR is a full path:

# this is where the containers were downloaded
config <- babelwhale::create_singularity_config(cache_dir = "MY_HOME_DIR/.singularity/cache")
babelwhale::set_default_config(config, permanent=FALSE)

models <- list()
for (meth in methods_selected) {
  models[[meth]] <- dynwrap::infer_trajectory(dataset, get(paste0('ti_', meth))(), give_priors = c("groups_id"), verbose = TRUE)
}

[dpschreiner]

sorry, i can't seem to be able to find further details here - would you be able to assist?

[dpschreiner]

how can i assess whether my singularity cache is correctly set up?

$ cd ~
$ find .singularity | grep -v blobs
.singularity
.singularity/cache
.singularity/cache/oci
.singularity/cache/oci/oci-put-blob371029300
.singularity/cache/oci/oci-put-blob407014447
.singularity/cache/oci/oci-layout
.singularity/cache/oci/index.json
.singularity/cache/oci-tmp
.singularity/cache/oci-tmp/fc54a7a1b9f78f38dbf36e0acaf0ee74ef9eba56aa5a9a8c5702a8a8e34aa815
.singularity/cache/oci-tmp/fc54a7a1b9f78f38dbf36e0acaf0ee74ef9eba56aa5a9a8c5702a8a8e34aa815/ti_slingshot_v1.0.3.sif
.singularity/cache/oci-tmp/4d1da3d4a0a4766fdb9feeef4c49bca5844df0d36259d2cb9a8d7fa9a9382539
.singularity/cache/oci-tmp/4d1da3d4a0a4766fdb9feeef4c49bca5844df0d36259d2cb9a8d7fa9a9382539/ti_slice_v0.9.9.01.sif
.singularity/cache/oci-tmp/93dad934d965258a3968346b5bfe47266ce41330576c5d42bd5e9d61492e1ec3
.singularity/cache/oci-tmp/93dad934d965258a3968346b5bfe47266ce41330576c5d42bd5e9d61492e1ec3/ti_pcreode_v0.9.9.01.sif
.singularity/cache/oci-tmp/8421d9a84432575381bfabd248f1eb56f3aa21d9d7cd2511583c68c9b7511d10
.singularity/cache/oci-tmp/8421d9a84432575381bfabd248f1eb56f3aa21d9d7cd2511583c68c9b7511d10/alpine_3.7.sif
.singularity/cache/oci-tmp/24980c21366515cb2e16ce89cd167237ba867dd75513a95ed47185e9ca9d6f27
.singularity/cache/oci-tmp/24980c21366515cb2e16ce89cd167237ba867dd75513a95ed47185e9ca9d6f27/ti_mst_v0.9.9.01.sif
.singularity/cache/oras
.singularity/cache/net
.singularity/cache/library
.singularity/cache/shub

[rcannood]

OK, now i'm hitting this issue from babelwhale:

Error in save(config, file = config_file, compress = "gz") : 
  'compress = "gz"' is invalid

perhaps just setting compress = TRUE would be sufficient?

If you were still having this issue with permanent = TRUE, could it be that babelwhale was not updated yet? devtools::install_github("dynverse/babelwhale")

[rcannood]

how can i assess whether my singularity cache is correctly set up?

This looks OK to me. Yesterday I pulled all of the ti_* images by running the following command in R:

dynwrap::get_ti_methods(evaluate = TRUE)

Afterwards, this is what my singularity cache looks like:

-bash-4.2$ find .singularity_cache | grep -v blobs
.singularity_cache
.singularity_cache/oci-tmp
.singularity_cache/oci-tmp/9f03596abb8aa24cf2fc82d1272eabba0b8816538960d4f467f57d827cc82884
.singularity_cache/oci-tmp/9f03596abb8aa24cf2fc82d1272eabba0b8816538960d4f467f57d827cc82884/ti_merlot_v0.9.9.01.sif
.singularity_cache/oci-tmp/d679fb5ae1c0c242430e6929bf8f2b651adef384b8d350f8f6dca1269c9ab5e1
.singularity_cache/oci-tmp/d679fb5ae1c0c242430e6929bf8f2b651adef384b8d350f8f6dca1269c9ab5e1/ti_grandprix_v0.9.9.01.sif
.singularity_cache/oci-tmp/0d6b740384f3daf52a6dc15e01d4dbdcfa06dd0ce813fac79b7a72d578016984
.singularity_cache/oci-tmp/0d6b740384f3daf52a6dc15e01d4dbdcfa06dd0ce813fac79b7a72d578016984/ti_sincell_v0.9.9.01.sif
.singularity_cache/oci-tmp/24980c21366515cb2e16ce89cd167237ba867dd75513a95ed47185e9ca9d6f27
.singularity_cache/oci-tmp/24980c21366515cb2e16ce89cd167237ba867dd75513a95ed47185e9ca9d6f27/ti_mst_v0.9.9.01.sif
.singularity_cache/oci-tmp/9c0ac1d78305ca0b4cee3288a913032ad213e34bce1d91607ee71d6d341e98ba
.singularity_cache/oci-tmp/9c0ac1d78305ca0b4cee3288a913032ad213e34bce1d91607ee71d6d341e98ba/ti_cellrouter_v0.9.9.01.sif
.singularity_cache/oci-tmp/6ac4869d08a3b51a27e6bb81ff8cbe8e1029a375854e5b5818deb5b107076d4f
.singularity_cache/oci-tmp/6ac4869d08a3b51a27e6bb81ff8cbe8e1029a375854e5b5818deb5b107076d4f/ti_matcher_v0.9.9.01.sif
.singularity_cache/oci-tmp/a534a2573ae18b891238c5c97dd82a09fd790fb29b1ca123a6493c10a3bb4b00
.singularity_cache/oci-tmp/a534a2573ae18b891238c5c97dd82a09fd790fb29b1ca123a6493c10a3bb4b00/ti_waterfall_v0.9.9.01.sif
.singularity_cache/oci-tmp/754ff729fe3b7475c170d7ab1817725a6e09c2ef360bc3b5a80b8b318e53e338
.singularity_cache/oci-tmp/754ff729fe3b7475c170d7ab1817725a6e09c2ef360bc3b5a80b8b318e53e338/ti_identity_v0.9.9.01.sif
.singularity_cache/oci-tmp/5f6ec7e960e172d65f71b6c2b9b883786bed3bf6e1be815f08ae8d16a149047a
.singularity_cache/oci-tmp/5f6ec7e960e172d65f71b6c2b9b883786bed3bf6e1be815f08ae8d16a149047a/ti_slicer_v0.9.9.01.sif
.singularity_cache/oci-tmp/b1899b5611e58990318fe069276e1ca121a696496a514e3ad19ce0add2fbdaf3
.singularity_cache/oci-tmp/b1899b5611e58990318fe069276e1ca121a696496a514e3ad19ce0add2fbdaf3/ti_celltree_gibbs_v0.9.9.01.sif
.singularity_cache/oci-tmp/9599794d86fd06e1875ef7c1e96d7501690c70379112ec0d583d345bdf528b6d
.singularity_cache/oci-tmp/9599794d86fd06e1875ef7c1e96d7501690c70379112ec0d583d345bdf528b6d/ti_paga_tree_v0.9.9.06.sif
.singularity_cache/oci-tmp/afe1b85f78a36059ab8d003e2fe33a08ddc6dd89fb06e1a42d42babea880b4bf
.singularity_cache/oci-tmp/afe1b85f78a36059ab8d003e2fe33a08ddc6dd89fb06e1a42d42babea880b4bf/ti_mfa_v0.9.9.01.sif
.singularity_cache/oci-tmp/05cbb67f0ead3e3ffc661de2eac7c3c22e117b0fee1ad3d6e26cb7898454a422
.singularity_cache/oci-tmp/05cbb67f0ead3e3ffc661de2eac7c3c22e117b0fee1ad3d6e26cb7898454a422/ti_projected_monocle_v0.9.9.01.sif
.singularity_cache/oci-tmp/c37ceef6a3029330f78682da244fbe9be5c6aceb7749e64ed41353a677a5f249
.singularity_cache/oci-tmp/c37ceef6a3029330f78682da244fbe9be5c6aceb7749e64ed41353a677a5f249/ti_fateid_v0.9.9.01.sif
.singularity_cache/oci-tmp/5a98279695dca4d50ad447ad0aa0e65fb0b1927ae3ad16f7f31d987533aef483
.singularity_cache/oci-tmp/5a98279695dca4d50ad447ad0aa0e65fb0b1927ae3ad16f7f31d987533aef483/ti_celltree_maptpx_v0.9.9.01.sif
.singularity_cache/oci-tmp/7daf03b54faf1b51097d2d8c69a781bb291d4e471d1627fb5b7816a62401e046
.singularity_cache/oci-tmp/7daf03b54faf1b51097d2d8c69a781bb291d4e471d1627fb5b7816a62401e046/ti_periodpc_v0.9.9.01.sif
.singularity_cache/oci-tmp/2d431a4f9fc3a2010292a43d7d54b13b3b0121d87d423e25b1c0bebf3a7c1a17
.singularity_cache/oci-tmp/2d431a4f9fc3a2010292a43d7d54b13b3b0121d87d423e25b1c0bebf3a7c1a17/ti_gpfates_v0.9.9.01.sif
.singularity_cache/oci-tmp/2519b29de4de8c36d3990f5399a85d2755f55ba7343eaef7afbfe7bed79cbdcf
.singularity_cache/oci-tmp/2519b29de4de8c36d3990f5399a85d2755f55ba7343eaef7afbfe7bed79cbdcf/ti_scoup_v0.9.9.01.sif
.singularity_cache/oci-tmp/8163f6db89898f8961286ecfc7f3ba48cbce577859d6f20106610cfe3524f544
.singularity_cache/oci-tmp/8163f6db89898f8961286ecfc7f3ba48cbce577859d6f20106610cfe3524f544/ti_scorpius_v1.0.0.01.sif
.singularity_cache/oci-tmp/6e73c2c646b243b7611a0f8e5b4708bcbb6e5769d67b9994f687b70fefec818a
.singularity_cache/oci-tmp/6e73c2c646b243b7611a0f8e5b4708bcbb6e5769d67b9994f687b70fefec818a/ti_elpicycle_v0.9.9.01.sif
.singularity_cache/oci-tmp/57cd996da2febb3172aaf064cc70e7da0d0ef545ee8255c2afcd33e81b907a86
.singularity_cache/oci-tmp/57cd996da2febb3172aaf064cc70e7da0d0ef545ee8255c2afcd33e81b907a86/ti_scuba_v0.9.9.01.sif
.singularity_cache/oci-tmp/f55d067615907223a43cb4397b62be3fb403b54647a5411e97305278af5ebc40
.singularity_cache/oci-tmp/f55d067615907223a43cb4397b62be3fb403b54647a5411e97305278af5ebc40/ti_projected_slingshot_v0.9.9.01.sif
.singularity_cache/oci-tmp/68fb81ed7e0d7115cab4b260d919b43520730c9a5f1a615914c57e4696a5765e
.singularity_cache/oci-tmp/68fb81ed7e0d7115cab4b260d919b43520730c9a5f1a615914c57e4696a5765e/ti_monocle_ddrtree_v0.9.9.02.sif
.singularity_cache/oci-tmp/352778ee6bc7d4723085df6bc67330cdd8a6b4449419d11b4a2f2360ce5755c1
.singularity_cache/oci-tmp/352778ee6bc7d4723085df6bc67330cdd8a6b4449419d11b4a2f2360ce5755c1/ti_ouijaflow_v0.9.9.01.sif
.singularity_cache/oci-tmp/f666eac144ae317d77b535a5833b5b76d4ae7048c02de099c5acb7ae89b068fb
.singularity_cache/oci-tmp/f666eac144ae317d77b535a5833b5b76d4ae7048c02de099c5acb7ae89b068fb/ti_mpath_v0.9.9.01.sif
.singularity_cache/oci-tmp/707ef69e67b3709bacc1be23ea3dea333c882588ca29f01b6a6d6e7fe5b3f9d0
.singularity_cache/oci-tmp/707ef69e67b3709bacc1be23ea3dea333c882588ca29f01b6a6d6e7fe5b3f9d0/ti_random_v0.9.9.01.sif
.singularity_cache/oci-tmp/cb735ed34235a98579144dd61323ac80b45902c016b45a4606964e7ca0bf31bc
.singularity_cache/oci-tmp/cb735ed34235a98579144dd61323ac80b45902c016b45a4606964e7ca0bf31bc/ti_raceid_stemid_v0.9.9.01.sif
.singularity_cache/oci-tmp/fc54a7a1b9f78f38dbf36e0acaf0ee74ef9eba56aa5a9a8c5702a8a8e34aa815
.singularity_cache/oci-tmp/fc54a7a1b9f78f38dbf36e0acaf0ee74ef9eba56aa5a9a8c5702a8a8e34aa815/ti_slingshot_v1.0.3.sif
.singularity_cache/oci-tmp/bc92bbef27bd0bdabb82556eacaeaf1b2d26b6ddb4a3fa72e1eaf24fa6f018fd
.singularity_cache/oci-tmp/bc92bbef27bd0bdabb82556eacaeaf1b2d26b6ddb4a3fa72e1eaf24fa6f018fd/ti_error_v0.9.9.01.sif
.singularity_cache/oci-tmp/33da227b01d741fc23463e8b7f67d409b865b2bac2a7416caf4debbf01361ed2
.singularity_cache/oci-tmp/33da227b01d741fc23463e8b7f67d409b865b2bac2a7416caf4debbf01361ed2/ti_wishbone_v0.9.9.01.sif
.singularity_cache/oci-tmp/7157d9629035291dae29b12c3c7bd06cdd088e28c0d6274b4669dcae0bddb108
.singularity_cache/oci-tmp/7157d9629035291dae29b12c3c7bd06cdd088e28c0d6274b4669dcae0bddb108/ti_monocle_ica_v0.9.9.01.sif
.singularity_cache/oci-tmp/f9f6fd5e0bcd4b2f39b774a58e0d89a669211f62b3f632da7bb364de8b495f4d
.singularity_cache/oci-tmp/f9f6fd5e0bcd4b2f39b774a58e0d89a669211f62b3f632da7bb364de8b495f4d/ti_phenopath_v0.9.9.01.sif
.singularity_cache/oci-tmp/fa4de78415877271d9d46b9888cd8eac75bab095b235f39332fe89de493829a9
.singularity_cache/oci-tmp/fa4de78415877271d9d46b9888cd8eac75bab095b235f39332fe89de493829a9/ti_dpt_v0.9.9.01.sif
.singularity_cache/oci-tmp/c128606cd42b0b0acbe0b88530b749e1f101329d8b7897a67b7a9485fb6f21bf
.singularity_cache/oci-tmp/c128606cd42b0b0acbe0b88530b749e1f101329d8b7897a67b7a9485fb6f21bf/ti_forks_v0.9.9.01.sif
.singularity_cache/oci-tmp/4c42b9ff47c4f51173ab0aba58cb2e72ca3e704c3e0c4e6701ff8339ab0f64cd
.singularity_cache/oci-tmp/4c42b9ff47c4f51173ab0aba58cb2e72ca3e704c3e0c4e6701ff8339ab0f64cd/ti_calista_v0.9.9.01.sif
.singularity_cache/oci-tmp/990f4b147c88e7b274706fa747bd681e0ad179e3270c79fbf8093dcd76a9c1e0
.singularity_cache/oci-tmp/990f4b147c88e7b274706fa747bd681e0ad179e3270c79fbf8093dcd76a9c1e0/ti_projected_dpt_v0.9.9.01.sif
.singularity_cache/oci-tmp/faad711690c5f84476679d6343212cbd09b2e9c29e4b2fd96f2c0078b4442e19
.singularity_cache/oci-tmp/faad711690c5f84476679d6343212cbd09b2e9c29e4b2fd96f2c0078b4442e19/ti_tscan_v0.9.9.01.sif
.singularity_cache/oci-tmp/a5e3f171bef830a96207fc2f9367409e63e4f2618de904447a4bb9679b21dd65
.singularity_cache/oci-tmp/a5e3f171bef830a96207fc2f9367409e63e4f2618de904447a4bb9679b21dd65/ti_scimitar_v0.9.9.01.sif
.singularity_cache/oci-tmp/4d1da3d4a0a4766fdb9feeef4c49bca5844df0d36259d2cb9a8d7fa9a9382539
.singularity_cache/oci-tmp/4d1da3d4a0a4766fdb9feeef4c49bca5844df0d36259d2cb9a8d7fa9a9382539/ti_slice_v0.9.9.01.sif
.singularity_cache/oci-tmp/29acf0a62a7e0673b77f640b7971e507316016e9af1c981f039b04341e8f1b51
.singularity_cache/oci-tmp/29acf0a62a7e0673b77f640b7971e507316016e9af1c981f039b04341e8f1b51/ti_urd_v0.9.9.01.sif
.singularity_cache/oci-tmp/8e54555872882d214286454210a5506e30a26cd9cb1e87425056adea501f2ea7
.singularity_cache/oci-tmp/8e54555872882d214286454210a5506e30a26cd9cb1e87425056adea501f2ea7/ti_angle_v0.9.9.02.sif
.singularity_cache/oci-tmp/601795ad4ef802babdc91eed792bc3e5d73f037e689ae4b1dc537e1efa6b4d73
.singularity_cache/oci-tmp/601795ad4ef802babdc91eed792bc3e5d73f037e689ae4b1dc537e1efa6b4d73/ti_elpigraph_v0.9.9.01.sif
.singularity_cache/oci-tmp/cbd593b99de638093667560af4a540f4ef17538dd6ac7ad4f885d33d40a8a883
.singularity_cache/oci-tmp/cbd593b99de638093667560af4a540f4ef17538dd6ac7ad4f885d33d40a8a883/ti_recat_v0.9.9.01.sif
.singularity_cache/oci-tmp/80643e1d7e7dd21e377d93357aa2727581ac6376c46e1586b517f78888cbd514
.singularity_cache/oci-tmp/80643e1d7e7dd21e377d93357aa2727581ac6376c46e1586b517f78888cbd514/ti_paga_v0.9.9.05.sif
.singularity_cache/oci-tmp/90863893149220eff91cc1eeb4c6161ade07304b6831115a285a81c8616cc382
.singularity_cache/oci-tmp/90863893149220eff91cc1eeb4c6161ade07304b6831115a285a81c8616cc382/ti_projected_tscan_v0.9.9.01.sif
.singularity_cache/oci-tmp/b1e2edc5c440a33afb79bf1dd09a9d620d522761554b16ec2959c399986c6fc8
.singularity_cache/oci-tmp/b1e2edc5c440a33afb79bf1dd09a9d620d522761554b16ec2959c399986c6fc8/ti_wanderlust_v0.9.9.01.sif
.singularity_cache/oci-tmp/9badf7bef89edbcc637c376fdcbc40b26a150f455cc12deb9728850b9bce9fe1
.singularity_cache/oci-tmp/9badf7bef89edbcc637c376fdcbc40b26a150f455cc12deb9728850b9bce9fe1/ti_celltree_vem_v0.9.9.01.sif
.singularity_cache/oci-tmp/d1a59e0a2740d9f24617941420911049b08743b23b1deb66896bf2448fbc73f9
.singularity_cache/oci-tmp/d1a59e0a2740d9f24617941420911049b08743b23b1deb66896bf2448fbc73f9/ti_topslam_v0.9.9.01.sif
.singularity_cache/oci-tmp/a2cd946f86e04be7d4f2478da2e3edf79012bfa936e1392d67249e370b27270c
.singularity_cache/oci-tmp/a2cd946f86e04be7d4f2478da2e3edf79012bfa936e1392d67249e370b27270c/ti_celltrails_v0.9.9.01.sif
.singularity_cache/oci-tmp/0b5aba6839e7fd70d8b430aec3b3512154c076559ad68a36da10a7dd80f672cd
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[rcannood]

here is what i'm running, where MY_HOME_DIR is a full path:

config <- babelwhale::create_singularity_config(cache_dir = "MY_HOME_DIR/.singularity/cache")
babelwhale::set_default_config(config, permanent=FALSE)

models <- list() for (meth in methods_selected) { models[[meth]] <- dynwrap::infertrajectory(dataset, get(paste0('ti', meth))(), give_priors = c("groups_id"), verbose = TRUE) }

This looks like it should work. If meth is a character, you might as well just run `dynwrap::infer_trajectory(dataset, meth, give_priors = "groups_id", verbose = TRUE)` and dynwrap will look up the corresponding ti_xxx function by running `dynwrap::get_ti_methods()`

If you set up your cache in the way that you did, and you try to run `ti_slingshot()`, what output do you get?

[dpschreiner]

i get the same error as initially reported on STDERR at the beginning of this issue:

> model <- dynwrap::infer_trajectory(dataset, 'slingshot', give_priors = c("groups_id"), 
                                     verbose = TRUE)
Running singularity exec 'docker://dynverse/ti_slingshot:v1.0.3' echo hi
Error in processx::run("singularity", c("exec", paste0("docker://", container_id),  :
  System command error

[beruhdejene]

Hi all, Running to similar issues here. I have tried the above suggestions to specify singularity cache dir. I have looked at the other thread as well (#44) but still hitting the same wall. I appreciate the help.

Running singularity exec 'docker://dynverse/ti_slingshot:v1.0.3' echo hi Error in processx::run("singularity", c("exec", paste0("docker://", container_id),