AriocP ApplicationException AriocBase/tuSetupN10.cu :
CUDA runtime API error 13: invalid device symbol Caller AriocP/tuGpu.cpp main
AriocP aborts
Did you try and run AriocP on a GPU without sufficient memory?
The documentation
Arioc release v1.04 (29-Jan-2015 12:34)
says it needs
"at least one NVidia GPU of compute capability 3.5 or greater, with at
least 5 gigabytes of GPU memory".
Work around
Check your GPU, eg with deviceQuery.
AriocE
ApplicationException (AriocE/../CppCommon/WinGlobalPtr.h): malloc failed to allocate 8589934592 bytes
AriocE aborts with exit status code 1.
With default settings,
a 12GB server does not seem to have enough memory.
It appears, by default, more than 16 gigabytes are needed.
Indeed the 1.04 documentation advises at least 72 gigabytes
for the human genome.
Work around
Check your server, eg look in file /proc/meminfo
AriocP
ApplicationException TaskUnit/tuBaseA.cpp unhandled C++ exception in TaskUnit worker thread
AriocP ends (1)
AriocP aborts.
Could be any exception inside one of the CPU host threads.
Most likely seems to be
thrust::system::detail::bad_alloc
std:e:bad_alloc: out of memory
No!! work around found
Is this a problem with running under linux?
Check your GPU, eg with nvidia-smi
Reducing batchSize may not help.
Increasing CUDAMINRESERVEDGLOBALMEMORY may not help.
AriocE /lib64/libc.so.6: version `GLIBC_2.14' not found (required by AriocE)
AriocE etc. abort with exit status code 1.
The linux executable AriocE needs version 2.14 (or later)
of the 64-bit GNU C run time library.
It is looking for it in /lib64/libc.so.6
but that file may contain an earlier version of libc.
Work around
See if /lib64/libc.so.6 exists,
e.g. using
ls -l /lib64/libc.so.6
(Typically it will exist and redirect to another library file whose
name suggests which version of the GNU library it contains.)
If libc-2.14.so or later exists somewhere else on your system it may
be possible to copy it or set up another redirection to point to it
or define the LD_LIBRARY_PATH environment variable to point to it
(in tcsh setenv LD_LIBRARY_PATH .:"$LD_LIBRARY_PATH")
however there may be other reasons why the Arioc* programs are not
compatible with your operating system.
Recompile all three programs for your system
(see also next section and
https://github.com/RWilton/Arioc/issues).
Compilation of AriocP fails
/usr/local/cuda-6.5/bin/nvcc -g -c -O2 -m64 -gencode arch=compute_35,code=sm_35 -Xcompiler -O2,-m64 -I /usr/local/cuda-6.5/include -o AriocP/tuSetupN.gpu.o AriocP/tuSetupN.cu
make: /usr/local/cuda-6.5/bin/nvcc: Command not found
Version 1.04 of Arioc assumes CUDA 6.5.
It will not compile with other versions of CUDA.
Work around
Edit src/makefile
to replace /cuda-6.5/ with /cuda/ (two cases)
and recompile following the instructions in src/makefile itself.
AriocP
ApplicationException AriocCommon/AriocAppMainBase.cpp missing element
AriocP aborts with exit status code 1.
Did you use
Arioc/Q/mason.paired.cfg
when you should have used
Arioc/A/mason.paired.cfg
Work around
Check .cfg file.
W.B.Langdon
Back
17 October 2015
(last update 20 Oct 2015)