[SOLVED] Problems compiling MODL on Cray XC40
Posted: Fri May 06, 2016 3:35 pm
Hi
I've been trying to compile and run NEURON on Cray XC40. After following the instructions from viewtopic.php?p=8803&sid=72065e087ffc59 ... 5f7a#p8803 I'm stuck.
I should probably add that the login node (where I compile stuff) have Sandy Bridge processors while compute nodes run on Haswell architecture.
I've compiled nmodl with flags for Sandy Bridge and added -fPIC after it complained that it needs it.
Then I've compiled NEURON itself (without nmodl) with flags for Haswell and -fPIC again.
I've tried testing it on the networks from "Translating network models to parallel hardware in NEURON". The ring network works fine. However, I've encountered some problems with the random connectivity network.
1. When I run nrnivmodl (having loaded the craype-haswell module, to make it compile with flags for compute node), it compiles, creates the necessary x86_64/.libs folder but for some reason creates only static libs, not the shared ones. I can convert them using the compiler, so it's not that much of a problem.
2. When I run the simulation (using SLURM), I get only a "Segmentation fault" without any further information.
The model runs on my home computer so it's not likely a typo. I'm really new to running NEURON in parallel, so I would really appreciate some help with debugging this.
Thank you.
I've been trying to compile and run NEURON on Cray XC40. After following the instructions from viewtopic.php?p=8803&sid=72065e087ffc59 ... 5f7a#p8803 I'm stuck.
I should probably add that the login node (where I compile stuff) have Sandy Bridge processors while compute nodes run on Haswell architecture.
I've compiled nmodl with flags for Sandy Bridge and added -fPIC after it complained that it needs it.
Then I've compiled NEURON itself (without nmodl) with flags for Haswell and -fPIC again.
I've tried testing it on the networks from "Translating network models to parallel hardware in NEURON". The ring network works fine. However, I've encountered some problems with the random connectivity network.
1. When I run nrnivmodl (having loaded the craype-haswell module, to make it compile with flags for compute node), it compiles, creates the necessary x86_64/.libs folder but for some reason creates only static libs, not the shared ones. I can convert them using the compiler, so it's not that much of a problem.
2. When I run the simulation (using SLURM), I get only a "Segmentation fault" without any further information.
The model runs on my home computer so it's not likely a typo. I'm really new to running NEURON in parallel, so I would really appreciate some help with debugging this.
Thank you.