Operating System: CentOS Linux release 7.4.1708 (Core)
Interface Version: R version 3.5.1, Rstudio 1.1.456
Compiler/Toolkit: gcc/7.2.0
Dear forum,
I’m executing code on a Linux computing cluster. Installing and loading rstan works without problems. However, when executing a stan() command:
f1 <- stan(model_code = mstr, data=dList, iter=10, init=0,
chains=1, seed=seed, chain_id=1, pars=paramInit)
(just for test purposes with 10 iterations), rstudio is aborted after ~30 seconds, giving the following errors:
[5771899.545016] traps: rsession[7206] trap invalid opcode ip:7f15b5b6ab3a sp:7fffe14f5430 error:0 in rstan.so[7f15b59f5000+361000]
[5771916.238232] traps: rsession[24955] trap invalid opcode ip:7f1fce4cab3a sp:7ffd2bd167e0 error:0 in rstan.so[7f1fce355000+361000]
[5771939.609177] traps: rsession[26429] trap invalid opcode ip:7f287b94db3a sp:7ffdeac7c3d0 error:0 in rstan.so[7f287b7d8000+361000]
[5772252.142301] traps: rsession[32637] trap invalid opcode ip:7fe3e3efcb3a sp:7ffc7bbeba50 error:0 in rstan.so[7fe3e3d87000+361000]
[5772342.611217] traps: rsession[23741] trap invalid opcode ip:7f847d1afb3a sp:7ffc20b54b50 error:0 in rstan.so[7f847d03a000+361000]
[5772475.612125] traps: rsession[31746] trap invalid opcode ip:7f8d58430b3a sp:7ffca83cf780 error:0 in rstan.so[7f8d582bb000+361000]
[5772497.630892] traps: rsession[12279] trap invalid opcode ip:7f37ea75db3a sp:7ffc7128bf40 error:0 in rstan.so[7f37ea5e8000+361000]
[5772861.781192] traps: rsession[13520] trap invalid opcode ip:7f557e4c9b3a sp:7fff03b34e40 error:0 in rstan.so[7f557e354000+361000]
[5774646.314608] rsession[29295]: segfault at 20 ip 00007fbb1ed8d560 sp 00007fff52159250 error 4 in Rcpp.so[7fbb1ed41000+5c000]
[5774891.787188] rsession[15764]: segfault at 20 ip 00007f91823bf560 sp 00007ffc72b800a0 error 4 in Rcpp.so[7f9182373000+5c000]
[5775072.730078] rsession[6620]: segfault at 20 ip 00007fb964448560 sp 00007ffdfdddcfa0 error 4 in Rcpp.so[7fb9643fc000+5c000]
The very same code has worked in the past when executed on a local (Windows) machine, so that shouldn’t be the problem. Also, I allocate 30 GB to the job, with the coding having worked properly with < 10 GB in the past.
The IT support of my institute suggested to post this question on this forum, as it might relate to memory access or segmentation problems when rstan compiles the model to stan…?
Thanks for any help!
Johannes