Illegal hardware instruction about squeakr HOT 9 CLOSED

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.

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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.

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Ah, thanks for the explanation. I'd appreciate the patch, if you're able to make it!

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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

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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

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$ 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?

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Can you check if "gzFile_s" is declared in your "/usr/include/zlib.h"?
If not you should upgrade your zlib package.

Thanks
Prashant

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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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