FATAL: container creation failed with singularity profile

[nhhaidee]

Bug report

Can not run pipeline with singularity profile

Expected behavior and actual behavior

Run pipeline (https://github.com/CFIA-NCFAD/nf-flu) with singularity profile but it failed with error

Steps to reproduce the problem

Run pipeline with -profile singularity

Program output

Command error: FATAL: container creation failed: mount /proc/self/fd/3->/usr/local/var/singularity/mnt/session/rootfs error: while mounting image /proc/self/fd/3: failed to find loop device: could not attach image file to loop device: no loop devices available

Environment

• Nextflow version: 23.04.1.5866
• Java version: openjdk 11.0.9.1-internal 2020-11-04
• Operating system: Ubuntu 22.04
• Bash version: 5.1.16(1)-release (x86_64-pc-linux-gnu)

Additional context

There is no problem with Docker profile

[nhhaidee]

The loop devices seem to be OK

dev/loop0 /dev/loop109 /dev/loop12 /dev/loop130 /dev/loop141 /dev/loop152 /dev/loop163 /dev/loop174 /dev/loop185 /dev/loop196 /dev/loop206 /dev/loop217 /dev/loop228 /dev/loop239 /dev/loop25 /dev/loop30 /dev/loop41 /dev/loop52 /dev/loop63 /dev/loop74 /dev/loop85 /dev/loop96 /dev/loop1 /dev/loop11 /dev/loop120 /dev/loop131 /dev/loop142 /dev/loop153 /dev/loop164 /dev/loop175 /dev/loop186 /dev/loop197 /dev/loop207 /dev/loop218 /dev/loop229 /dev/loop24 /dev/loop250 /dev/loop31 /dev/loop42 /dev/loop53 /dev/loop64 /dev/loop75 /dev/loop86 /dev/loop97 /dev/loop10 /dev/loop110 /dev/loop121 /dev/loop132 /dev/loop143 /dev/loop154 /dev/loop165 /dev/loop176 /dev/loop187 /dev/loop198 /dev/loop208 /dev/loop219 /dev/loop23 /dev/loop240 /dev/loop251 /dev/loop32 /dev/loop43 /dev/loop54 /dev/loop65 /dev/loop76 /dev/loop87 /dev/loop98 /dev/loop100 /dev/loop111 /dev/loop122 /dev/loop133 /dev/loop144 /dev/loop155 /dev/loop166 /dev/loop177 /dev/loop188 /dev/loop199 /dev/loop209 /dev/loop22 /dev/loop230 /dev/loop241 /dev/loop252 /dev/loop33 /dev/loop44 /dev/loop55 /dev/loop66 /dev/loop77 /dev/loop88 /dev/loop99 /dev/loop101 /dev/loop112 /dev/loop123 /dev/loop134 /dev/loop145 /dev/loop156 /dev/loop167 /dev/loop178 /dev/loop189 /dev/loop2 /dev/loop21 /dev/loop220 /dev/loop231 /dev/loop242 /dev/loop253 /dev/loop34 /dev/loop45 /dev/loop56 /dev/loop67 /dev/loop78 /dev/loop89 /dev/loop-control /dev/loop102 /dev/loop113 /dev/loop124 /dev/loop135 /dev/loop146 /dev/loop157 /dev/loop168 /dev/loop179 /dev/loop19 /dev/loop20 /dev/loop210 /dev/loop221 /dev/loop232 /dev/loop243 /dev/loop254 /dev/loop35 /dev/loop46 /dev/loop57 /dev/loop68 /dev/loop79 /dev/loop9 /dev/loop103 /dev/loop114 /dev/loop125 /dev/loop136 /dev/loop147 /dev/loop158 /dev/loop169 /dev/loop18 /dev/loop190 /dev/loop200 /dev/loop211 /dev/loop222 /dev/loop233 /dev/loop244 /dev/loop255 /dev/loop36 /dev/loop47 /dev/loop58 /dev/loop69 /dev/loop8 /dev/loop90 /dev/loop104 /dev/loop115 /dev/loop126 /dev/loop137 /dev/loop148 /dev/loop159 /dev/loop17 /dev/loop180 /dev/loop191 /dev/loop201 /dev/loop212 /dev/loop223 /dev/loop234 /dev/loop245 /dev/loop26 /dev/loop37 /dev/loop48 /dev/loop59 /dev/loop7 /dev/loop80 /dev/loop91 /dev/loop105 /dev/loop116 /dev/loop127 /dev/loop138 /dev/loop149 /dev/loop16 /dev/loop170 /dev/loop181 /dev/loop192 /dev/loop202 /dev/loop213 /dev/loop224 /dev/loop235 /dev/loop246 /dev/loop27 /dev/loop38 /dev/loop49 /dev/loop6 /dev/loop70 /dev/loop81 /dev/loop92 /dev/loop106 /dev/loop117 /dev/loop128 /dev/loop139 /dev/loop15 /dev/loop160 /dev/loop171 /dev/loop182 /dev/loop193 /dev/loop203 /dev/loop214 /dev/loop225 /dev/loop236 /dev/loop247 /dev/loop28 /dev/loop39 /dev/loop5 /dev/loop60 /dev/loop71 /dev/loop82 /dev/loop93 /dev/loop107 /dev/loop118 /dev/loop129 /dev/loop14 /dev/loop150 /dev/loop161 /dev/loop172 /dev/loop183 /dev/loop194 /dev/loop204 /dev/loop215 /dev/loop226 /dev/loop237 /dev/loop248 /dev/loop29 /dev/loop4 /dev/loop50 /dev/loop61 /dev/loop72 /dev/loop83 /dev/loop94 /dev/loop108 /dev/loop119 /dev/loop13 /dev/loop140 /dev/loop151 /dev/loop162 /dev/loop173 /dev/loop184 /dev/loop195 /dev/loop205 /dev/loop216 /dev/loop227 /dev/loop238 /dev/loop249 /dev/loop3 /dev/loop40 /dev/loop51 /dev/loop62 /dev/loop73 /dev/loop84 /dev/loop95

[Biocentric]

We have the same issue, singularity profile does not work on our cluster system. We looked at the solution proposed here:
sylabs/singularity#1499

But it does not yield a consistent solution for Nextflow. Test singularity containers will run after this intervention but no full Nextflow runs.

[Fiwx]

I have the same issue. Only test runs will work, but not full Nextflow runs. Here is the error:

FATAL: container creation failed: mount /proc/self/fd/4->/usr/local/var/singularity/mnt/session/rootfs error: while mounting image /proc/self/fd/4: failed to find loop device: could not attach image file to loop device: no loop devices available