From vicky.tzuyin.lai at gmail.com  Wed Jul 16 09:07:57 2014
From: vicky.tzuyin.lai at gmail.com (Vicky Lai)
Date: Wed, 16 Jul 2014 12:07:57 -0400
Subject: [Optseq-commits] Segmentation fault: 11
Message-ID: <8A0DD3E5-3691-48ED-9622-F7FE21231BCD@gmail.com>

Dear optseq developers,

I downloaded optseq2 and ran the following command line. I received some (error) messages that I don't understand. Can someone help? 

Here's my command line:

./optseq2 --ntp 192 --tr 1.875 --psdwin 0 13.125 --tnullmin 1.875 --polyfit 2 --ev evt1 1.875 6 --ev evt2 1.875 6 --ev evt3 1.875 6 --ev evt4 1.875 6 --ev evt5 1.875 6 --ev evt6 1.875 6 --ev evt7 1.875 6 --ev evt8 1.875 6 --evc 1 -1 0 0 0 0 0 0 --evc 0 0 1 -1 0 0 0 0 --evc 0 0 0 0 1 -1 0 0 --nkeep 6 --o vic1 --nsearch 10000

Here are the messages I received (The rank-deficiency message came out repeatedly):

/usr/pubsw/packages/vxl/1.9.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 41
/usr/pubsw/packages/vxl/1.9.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 41
/usr/pubsw/packages/vxl/1.9.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 41
/usr/pubsw/packages/vxl/1.9.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 41
99    1000     0.0   0.383043  0.383043  0.6979  2.68233  0.0562745  2.58249  2.7519  0.169416 697.5 10
INFO: searched 1000 iterations for 0.000556 hours
INFO: 500 iterations per second
INFO: 577/1000 schedules were ill-conditioned 
outstem = vic1


There are outputs though. I just don't know if I can trust the output schedules: 

Vicky$ ls
optseq2			vic1-002.par		vic1-004.par		vic1-006.par		vic1.sum vic1-001.par		vic1-003.par		vic1-005.par		vic1.log		vic1.xtxideal.mat

Vicky$ less vic1-001.par 

 0.0000    6    1.875   1.0000          evt6
 1.8750    0    1.875   1.0000          NULL 
 3.7500    2    1.875   1.0000          evt2
 5.6250    0    9.375   1.0000          NULL 
15.0000    1    1.875   1.0000          evt1
16.8750    0    1.875   1.0000          NULL 


I also tried --tsearch instead of --nsearch. I specified 8 hours with the intention of letting it run overnight. However, it says "Segmentation fault: 11". Does someone know what this means and what the solution is? Does it have to do with my computer? My work computer is Mac 10.8.5, mountain lion.

Thanks!!

Vicky