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Compilation fails on Smith-Waterman plugin (Read 210 times)
Jun 3rd, 2018 at 8:08pm

Louis Becquey   Offline
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France

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Hello,
I am trying to build Ugene from source (because i want it to work with Cuda).

Something goes wrong with the Smith-Waterman plugin that makes the build fail, it looks like a path issue:

qmake -r
Code:
...
Reading /home/persalteas/ugene-1.30.0/src/plugins/smith_waterman/smith_waterman.pro
QDir::mkpath: Empty or null file name
WARNING: nvzz: Cannot access directory ''
... 



And if i try to build it anyway, it works well for a while, and finally fails on the Smith-Waterman plugin again:

make
Code:
...

nvcc -m 32 -g -G -Xcompiler -Zi,-MD -Xlinker /DEBUG -c -I -Isrc -I_tmp -I../../include -I../../corelibs/U2View/_tmp -L -lcudart -o _tmp/obj/release/sw_cuda.o src/sw_cuda.cu
nvcc warning : Compiling in the 32-bit mode when the host compiler targets x86 or x86_64 is no longer supported on Linux
gcc-6: error: unrecognized command line option ‘-Zi’; did you mean ‘-Z’?
Makefile.Release:292: recipe for target '_tmp/obj/release/sw_cuda.o' failed
 



I tried to edit src/plugins/smith_waterman/smith_waterman.pri to force -m 64 (removed the warning about 32 bit mode) and to replace -Zi by -Z. The compilation went a bit further, but failed again:

Code:
make[1] : entering directory « /home/persalteas/ugene-1.30.0/src/plugins/smith_waterman »
/usr/lib/qt5/bin/qmake -o Makefile smith_waterman.pro
QDir::mkpath: Empty or null file name
WARNING: nvzz: Cannot access directory ''
 


and then linking fails.


Additional info:
- Issue observed on two different machines:
  • a Centos 7 workstation with 8 core Intel Xeon, GCC 5, Nvidia driver 390, CUDA 9.2,
  • an Ubuntu 18.04 with 16-core AMD Ryzen, GCC 6, Nvidia 390 driver, CUDA 9.1.

- Used the source of UGENE 1.30, downloaded from here : ugene.unipro.ru/downloads/ugene_get_latest_source.html


Any idea what to do ? Any help would be appreciated, thanks in advance !

 
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Reply #1 - Jun 4th, 2018 at 2:26pm

Olga Golosova   Offline
YaBB Administrator

Posts: 222
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Hello, Louis!

Thanks for your request!

We were able to reproduce the issue. We're currently trying to solve it and will write you as soon as there are news on that.
 
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Reply #2 - Jun 6th, 2018 at 12:23am

Louis Becquey   Offline
YaBB Newbies
France

Gender: male
Posts: 2
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Thank you, i am waiting to hear from you, then.  Smiley
 
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Reply #3 - Jun 7th, 2018 at 5:44pm

Olga Golosova   Offline
YaBB Administrator

Posts: 222
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Hi Louis!

Quote:
Thank you, i am waiting to hear from you, then.

Yeap, sorry for the delay! We were able to reproduce the issue, but we haven't found a solution yet. We'll spend some time more to investigate the issue.

 
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Reply #4 - Jun 20th, 2018 at 6:53pm

Olga Golosova   Offline
YaBB Administrator

Posts: 222
*****
 
Hi again!

I'm writing to inform you that we're still working on the issue. We fixed the compilation issues, but we have some problems with testing the issue on a Linux machine. Hopefully, we'll solve them in the nearest future.

Sorry again for the delay!
 
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