Thank you for the suggestion, I now get the error pasted below. It looks like a problem with allocating memory…
This could be related, or completely due to the fact, that something is taking all of the available storage in /usr/ while this is trying to run. I don’t understand why if I’m using --cleanEnv. It’s hard to track down what it is since the script clears it all once it fails. Singularity was installed to the root directory, I moved it to a drive with more space and I’m still getting the same error.
The singularity image, data folder, output folder, and working folder are all on drives with plenty of space. The machine has >150GB of RAM and my understanding is that singularity utilizes all available resources.
I tried (Error using bids_validator) and I still get the same error. This is what I get after running the patch.
npm WARN saveError ENOENT: no such file or directory, open ‘/data2/users/liz/MLINDIV/fmriPrep/package.json’
npm notice created a lockfile as package-lock.json. You should commit this file.
npm WARN enoent ENOENT: no such file or directory, open ‘/data2/users/liz/MLINDIV/fmriPrep/package.json’
npm WARN fmriPrep No description
npm WARN fmriPrep No repository field.
npm WARN fmriPrep No README data
npm WARN fmriPrep No license field.
added 135 packages from 127 contributors and audited 196 packages in 3.649s
found 0 vulnerabilities
And this is what I get after running fmriPrep
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
<— Last few GCs —>
[10722:0x2fd0110] 528492 ms: Mark-sweep 1208.4 (1215.3) -> 1208.4 (1214.3) MB, 8.9 / 0.0 ms (average mu = 0.998, current mu = 0.003) last resort GC in old space requested
[10722:0x2fd0110] 528500 ms: Mark-sweep 1208.4 (1214.3) -> 1208.4 (1214.3) MB, 8.2 / 0.0 ms (average mu = 0.998, current mu = 0.002) last resort GC in old space requested
<— JS stacktrace —>
==== JS stack trace =========================================
0: ExitFrame [pc: 0x164a15e5be1d]
Security context: 0x10c2b139e6e1
1: stringSlice(aka stringSlice) [0x33b48bb58c01] [buffer.js:594] [bytecode=0x3d6e6a10c1f9 offset=91](this=0x37026c9026f1 ,buf=0x1625c57ebf61 ,encoding=0x10c2b13bcbe9 <String: utf8>,start=0,end=278649801)
2: toString [0x2e592599d4a1] [buffer.js:667] [bytecode=0x1625c57efaf1 offset=145](this=0x1625c57ebf61…
1: 0x8db900 node::Abort() [bids-validator]
2: 0x8db94c [bids-validator]
3: 0xad6c1e v8::Utils::ReportOOMFailure(v8::internal::Isolate*, char const*, bool) [bids-validator]
4: 0xad6e54 v8::internal::V8::FatalProcessOutOfMemory(v8::internal::Isolate*, char const*, bool) [bids-validator]
5: 0xec44e2 [bids-validator]
6: 0xed3cff v8::internal::Heap::AllocateRawWithRetryOrFail(int, v8::internal::AllocationSpace, v8::internal::AllocationAlignment) [bids-validator]
7: 0xea38ab v8::internal::NewRawTwoByteString(int, v8::internal::PretenureFlag) [bids-validator]
8: 0xea41b2 v8::internal::NewStringFromUtf8(v8::internal::Vector, v8::internal::PretenureFlag) [bids-validator]
9: 0xae4c69 v8::String::NewFromUtf8(v8::Isolate*, char const*, v8::NewStringType, int) [bids-validator]
10: 0x99d9f8 node::StringBytes::Encode(v8::Isolate*, char const*, unsigned long, node::encoding, v8::Localv8::Value) [bids-validator]
11: 0x8f7ac8 [bids-validator]
12: 0xb5f33f [bids-validator]
13: 0xb5fea9 v8::internal::Builtin_HandleApiCall(int, v8::internal::Object**, v8::internal::Isolate) [bids-validator]
Traceback (most recent call last):
File “/usr/local/miniconda/bin/fmriprep”, line 11, in
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py”, line 354, in main
validate_input_dir(exec_env, opts.bids_dir, opts.participant_label)
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py”, line 535, in validate_input_dir
subprocess.check_call([‘bids-validator’, bids_dir, ‘-c’, temp.name])
File “/usr/local/miniconda/lib/python3.7/subprocess.py”, line 341, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command ‘[‘bids-validator’, ‘/work/dataBids’, ‘-c’, ‘/tmp/tmpj5dq_11u’]’ died with <Signals.SIGABRT: 6>.
Sentry is attempting to send 1 pending error messages
Waiting up to 2.0 seconds