Error compiling GMAP
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4.7 years ago

I'm trying to compile GMAP on ubuntu but when I run the make command I get this output:

collect2: error: ld returned 1 exit status
Makefile:3471: fallo en las instrucciones para el objetivo 'gmap.avx2'
make[2]: *** [gmap.avx2] Error 1
make[2]: se sale del directorio '/home/fml/Descargas/TFG/FRESA/gmap-2018-03-11/src'
Makefile:3314: fallo en las instrucciones para el objetivo 'all'
make[1]: *** [all] Error 2
make[1]: se sale del directorio '/home/fml/Descargas/TFG/FRESA/gmap-2018-03-11/src'
Makefile:431: fallo en las instrucciones para el objetivo 'all-recursive'
make: *** [all-recursive] Error 1

I don't know where the error is but the files in that directory were not compiled. Sorry for the spanish language, if you don't understand it let me know and I will translate. Thank you in advance.

GMAP ubuntu error • 1.7k views
Entering edit mode

Which version of GMAP, Ubuntu and GCC? How are you compiling GMAP - just make? Are there other error messages, probably appearing before the ones you posted? What is the output of cat /proc/cpuinfo | grep "avx2"?

Finally, can't you install GMAP from Ubuntu repositories:

sudo apt-get install gmap
Entering edit mode

GMAP - latest version Ubuntu - 16.4.04 (virtual machine) GCC - 5.4.0

I'm just following the setup instructions on the README file:

make check
make install

There were no errors before

The output of that line is:

flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts mmx fxsr sse sse2 ss nx pdpe1gb rdtscp constant_tsc arch_perfmon pebs bts xtopology tsc_reliable nonstop_tsc cpuid aperfmperf pni pclmulqdq ssse3 fma pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor abm cpuid_fault epb retpoline fsgsbase tsc_adjust bmi1 avx2 smep bmi2 invpcid xsaveopt dtherm ida arat pln pts

I installed GMAP from repositories before, but that way I didn't find the file to entablish some paths (anyway I'll install it from repositories using default paths if the error remains)

Entering edit mode

16.4.04 (virtual machine)

Probably this is the cause of the problem (are you using VirtualBox?):

Try ./configure --with-simd-level=sse4.2.

Entering edit mode

Sorry for answering that late. I'm using vmware and the error remains. I'll try to borrow a server or install linux. Thank you for all your help.


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