vfonov
commented
10 years ago Can't reproduce this on my VM what are your configuration options ? Are you using system-supplied libraries or building everything internally?
Closed carlohamalainen closed 10 years ago
vfonov
commented
10 years ago Can't reproduce this on my VM what are your configuration options ? Are you using system-supplied libraries or building everything internally?
carlohamalainen
commented
10 years ago I installed a minimal Debian Wheezy 64bit system, then added these packages:
sudo apt-get install cmake cmake-curses-gui
sudo apt-get install \
build-essential g++ \
cmake cmake-curses-gui \
bison flex \
freeglut3 freeglut3-dev \
libxi6 libxi-dev libxmu6 libxmu-dev libxmu-headersCloned the repo, etc:
git clone --recursive git://github.com/BIC-MNI/minc-toolkit.git minc-toolkit
cd minc-toolkit
rm -fr build
mkdir build
cd build
ccmake .. # hit 'c'
# go down to MT_BUILD_SHARED_LIBS, hit enter to turn 'ON'
# hit 'c'
# hit 'g'
#
make &> make.logSo changing MT_BUILD_SHARED_LIBS was the only thing that I did differently. I need this option to get pyminc to work.
Also I can't reproduce this on my Debian Wheezy laptop (Lenovo Carbon X1), it all builds fine.
Maybe dodgy ram on my Amazon VM? Or something to do with the CPU architecture?
$ cat /proc/cpuinfo
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 44
model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
stepping : 2
microcode : 0x13
cpu MHz : 1999.975
cache size : 12288 KB
physical id : 0
siblings : 1
core id : 0
cpu cores : 1
apicid : 0
initial apicid : 50
fpu : yes
fpu_exception : yes
cpuid level : 11
wp : yes
flags : fpu de tsc msr pae cx8 sep cmov pat clflush mmx fxsr sse sse2 ss ht syscall nx lm constant_tsc up rep_good nopl nonstop_tsc pni pclmulqdq ssse3 cx16 pcid sse4_1 sse4_2 popcnt aes hypervisor lahf_lm
bogomips : 3999.95
clflush size : 64
cache_alignment : 64
address sizes : 40 bits physical, 48 bits virtual
power management:how much memory does VM have ?
carlohamalainen
commented
10 years ago 1.7Gb, should be enough? I'll try building again with some swap space enabled. The other VM where it built ok has only 600Mb of ram and no swap.
carlohamalainen
commented
10 years ago I can replicate the segfault in a VirtualBox VM on my laptop. I could export the VM to an ova file if you want to try it yourself.
vfonov
commented
10 years ago ok, let's try
carlohamalainen
commented
10 years ago OK, I've emailed you a url to the VirtualBox ova file.
vfonov
commented
10 years ago ok, thank you I found the bug and fixed it : https://github.com/BIC-MNI/minc-tools/commit/f5d91cb16fcf7b82f43816cc5f4264fb4103c843
carlohamalainen
commented
10 years ago Great, can confirm that it now builds without errors on my Amazon EC2 instance.
Thanks.
Hi,
I can't build the minc-toolkit on my Debian Wheezy 64bit VM (it does build fine on another Ubuntu 13.10 VM though).
The error:
If I go into mni_autoreg/Testing I can trigger the segfault and get more details. Turns out there is a "double free or corruption" in mincresample: