Comments (9)
Hey John,
Squeakr uses a CQF as the underlying data structure to count kmers. The CQF code uses two new instructions that were introduced in Intel Haswell (4th generation) line of CPUs.
I guess the machine you are using doesn't have a Haswell or newer CPU. That's why you are getting an "illegal hardware instruction" issue.
from squeakr.
I will try to release a patch so that the code can use the C implementation of the new instructions if the underlying hardware doesn't support them.
from squeakr.
Ah, thanks for the explanation. I'd appreciate the patch, if you're able to make it!
from squeakr.
Hey John,
I have pushed a new commit for the code to work on older-than-Haswell CPUs. The REAMDE is also updated with instructions on how to build.
Thanks
Prashant
from squeakr.
Thanks for that!
I'm now getting a compile error, which I guess is due to missing zlib includes?
In file included from main.cc:49:0:
reader.h:35:21: error: ‘gzFile_s’ has not been declared
reader(FILE *in, gzFile_s *in_gzip, BZFILE *in_bzip2, int bzerror);
^
reader.h:38:4: error: ‘gzFile_s’ does not name a type
gzFile_s *in_gzip = nullptr;
^
I've got zlib.h
in /usr/include
which should be ok? I noticed some of the zlib stuff changed with the recent commit
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Can you check the version of zlib and bzip2 on your machine?
Here is what I have:
$ apt-cache policy zlib1g-dev
zlib1g-dev:
Installed: 1:1.2.8.dfsg-2ubuntu4
Candidate: 1:1.2.8.dfsg-2ubuntu4
Version table:
*** 1:1.2.8.dfsg-2ubuntu4 500
500 http://ca.archive.ubuntu.com/ubuntu xenial/main amd64 Packages
100 /var/lib/dpkg/status
$ apt-cache policy bzip2
bzip2:
Installed: 1.0.6-8
Candidate: 1.0.6-8
Version table:
*** 1.0.6-8 500
500 http://ca.archive.ubuntu.com/ubuntu xenial/main amd64 Packages
100 /var/lib/dpkg/status
from squeakr.
$ apt-cache policy zlib1g-dev
zlib1g-dev:
Installed: 1:1.2.3.4.dfsg-3ubuntu4
Candidate: 1:1.2.3.4.dfsg-3ubuntu4
Version table:
*** 1:1.2.3.4.dfsg-3ubuntu4 0
500 http://www.mirrorservice.org/sites/archive.ubuntu.com/ubuntu/ precise/main amd64 Packages
100 /var/lib/dpkg/status
$ apt-cache policy bzip2
bzip2:
Installed: 1.0.6-1
Candidate: 1.0.6-1
Version table:
*** 1.0.6-1 0
500 http://www.mirrorservice.org/sites/archive.ubuntu.com/ubuntu/ precise/main amd64 Packages
100 /var/lib/dpkg/status
Do you think the zlib version is too low?
from squeakr.
Can you check if "gzFile_s" is declared in your "/usr/include/zlib.h"?
If not you should upgrade your zlib package.
Thanks
Prashant
from squeakr.
Hi Prashant,
I have installed zlib 1.2.11, and now squeakr has compiled and runs correctly. Thanks so much for your help! I look forward to using the tool.
John
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Related Issues (20)
- Doc command line doesn't much help HOT 3
- Add a --version or -v flag
- Command line parsing seems to be broken in exact branch HOT 1
- squeakr-query "Not Find: 0" HOT 3
- Plans to support FASTA? HOT 2
- lognumslots.sh sometimes underestimates the required number of slots HOT 2
- Segmentation fault while counting human genome HOT 7
- Update release? HOT 6
- Can't install on OSX, expected identifier FREAD HOT 3
- boost/thread/thread.hpp error installing on macOS HOT 3
- Release 0.6 prints 1.0 with help -v HOT 1
- MacOS: use of undeclared identifier 'posix_fallocate' HOT 3
- gqf/partitioned_counter.c:15:10: fatal error: 'sys/sysinfo.h' file not found
- endless loop in /src/count.cc HOT 1
- /src/count.cc can silently drop input files HOT 2
- Illegal instruction error HOT 4
- long reads?
- Assertion `new_value < current_remainder' failed. HOT 5
- Segmentation fault
- Error opening file for serializing.: Is a directory HOT 3
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