Error compiling GMAP

Question

[Francisco Muñoz]

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.

[h.mon]

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

[Francisco Muñoz]

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

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

./configure
make
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 config.site to entablish some paths (anyway I'll install it from repositories using default paths if the error remains)

[h.mon]

16.4.04 (virtual machine)

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

https://askubuntu.com/questions/699077/how-to-enable-avx2-extensions-on-a-ubuntu-guest-in-virtualbox-5

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

[Francisco Muñoz]

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.