Error during SPRINGDB instalaltion

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Moderator: robpearc

carlos
Posts: 1
Joined: Thu Jul 15, 2021 3:03 pm

Error during SPRINGDB instalaltion

Post by carlos »

Hello,

Can you please help me?
I'm trying to install SPRINGDB locally and I got an error during the installation.
So, I individually compiled TMalign, TMScore successfully, but failed during the
NWalign compilation.

This is the command that is failing
f2py -c -m nwalign NWalign_wrapper.f

I attached the error message and the operating system information (please see below).

I'm using perl v5.28.0 and a virtual environment with Python 2.7.15 (and numpy 1.16.6).

Thanks
Carlos

ERROR MESSAGE
(venv) [kalyani@wulab NWalign]$ f2py -c -m nwalign NWalign_wrapper.f
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building extension "nwalign" sources
f2py options: []
f2py:> /tmp/tmpDxm237/src.linux-x86_64-2.7/nwalignmodule.c
creating /tmp/tmpDxm237/src.linux-x86_64-2.7
Reading fortran codes...
Reading file 'NWalign_wrapper.f' (format:fix,strict)
{'this': 'intent', 'after': '(in) seq_1(s1len), seq_2,(s2len)', 'before': ''}
Line #31 in NWalign_wrapper.f:" intent(in) seq_1(s1len), seq_2,(s2len)"
analyzeline: no name pattern found in intent statement for '(s2len)'. Skipping.
Traceback (most recent call last):
File "/home/kalyani/venv/bin/f2py", line 8, in <module>
sys.exit(main())
File "/home/kalyani/venv/lib/python2.7/site-packages/numpy/f2py/f2py2e.py", line 683, in main
run_compile()
File "/home/kalyani/venv/lib/python2.7/site-packages/numpy/f2py/f2py2e.py", line 650, in run_compile
setup(ext_modules=[ext])
File "/home/kalyani/venv/lib/python2.7/site-packages/numpy/distutils/core.py", line 171, in setup
return old_setup(**new_attr)
File "/home/kalyani/opt/python-2.7.15/lib/python2.7/distutils/core.py", line 151, in setup
dist.run_commands()
File "/home/kalyani/opt/python-2.7.15/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/home/kalyani/opt/python-2.7.15/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/home/kalyani/venv/lib/python2.7/site-packages/numpy/distutils/command/build.py", line 47, in run
old_build.run(self)
File "/home/kalyani/opt/python-2.7.15/lib/python2.7/distutils/command/build.py", line 127, in run
self.run_command(cmd_name)
File "/home/kalyani/opt/python-2.7.15/lib/python2.7/distutils/cmd.py", line 326, in run_command
self.distribution.run_command(command)
File "/home/kalyani/opt/python-2.7.15/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/home/kalyani/venv/lib/python2.7/site-packages/numpy/distutils/command/build_src.py", line 148, in run
self.build_sources()
File "/home/kalyani/venv/lib/python2.7/site-packages/numpy/distutils/command/build_src.py", line 165, in build_sources
self.build_extension_sources(ext)
File "/home/kalyani/venv/lib/python2.7/site-packages/numpy/distutils/command/build_src.py", line 325, in build_extension_sources
sources = self.f2py_sources(sources, ext)
File "/home/kalyani/venv/lib/python2.7/site-packages/numpy/distutils/command/build_src.py", line 562, in f2py_sources
['-m', ext_name]+f_sources)
File "/home/kalyani/venv/lib/python2.7/site-packages/numpy/f2py/f2py2e.py", line 425, in run_main
postlist = callcrackfortran(files, options)
File "/home/kalyani/venv/lib/python2.7/site-packages/numpy/f2py/f2py2e.py", line 329, in callcrackfortran
postlist = crackfortran.crackfortran(files)
File "/home/kalyani/venv/lib/python2.7/site-packages/numpy/f2py/crackfortran.py", line 3251, in crackfortran
readfortrancode(files, crackline)
File "/home/kalyani/venv/lib/python2.7/site-packages/numpy/f2py/crackfortran.py", line 501, in readfortrancode
dowithline(finalline)
File "/home/kalyani/venv/lib/python2.7/site-packages/numpy/f2py/crackfortran.py", line 796, in crackline
analyzeline(m, pat[1], line)
File "/home/kalyani/venv/lib/python2.7/site-packages/numpy/f2py/crackfortran.py", line 1184, in analyzeline
for e in markoutercomma(ll).split('@,@'):
File "/home/kalyani/venv/lib/python2.7/site-packages/numpy/f2py/crackfortran.py", line 833, in markoutercomma
assert not f, repr((f, line, l))
AssertionError: (-1, 'naa=23) !number of amino aci', 'naa=23) !number of amino aci')


OPERATING SYSTEM INFO

ot@wulab ~]# uname -a; lsb_release -a; head -n 25 /proc/cpuinfo; ulimit -a; free
Linux wulab.montefiore.org 4.18.0-240.22.1.el8_3.x86_64 #1 SMP Thu Apr 8 19:01:30 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
LSB Version: :core-4.1-amd64:core-4.1-noarch
Distributor ID: CentOS
Description: CentOS Linux release 8.3.2011

Release: 8.3.2011
Codename: n/a
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 85
model name : Intel(R) Xeon(R) Silver 4208 CPU @ 2.10GHz
stepping : 7
microcode : 0x5003006
cpu MHz : 1142.901
cache size : 11264 KB
physical id : 0
siblings : 8
core id : 0
cpu cores : 8
apicid : 0
initial apicid : 0
fpu : yes
fpu_exception : yes
cpuid level : 22
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch cpuid_fault epb cat_l3 cdp_l3 invpcid_single intel_ppin ssbd mba ibrs ibpb stibp ibrs_enhanced tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid cqm mpx rdt_a avx512f avx512dq rdseed adx smap clflushopt clwb intel_pt avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts pku ospke avx512_vnni md_clear flush_l1d arch_capabilities
bugs : spectre_v1 spectre_v2 spec_store_bypass swapgs taa itlb_multihit
bogomips : 4200.00

clflush size : 64
cache_alignment : 64
address sizes : 46 bits physical, 48 bits virtual
core file size (blocks, -c) unlimited
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 126127
max locked memory (kbytes, -l) 64
max memory size (kbytes, -m) unlimited
open files (-n) 1024
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) 126127
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited

total used free shared buff/cache available
Mem: 32346412 1619680 973172 38828 29753560 30220260
Swap: 16343036 116992 16226044
robpearc
Posts: 40
Joined: Sun May 02, 2021 5:49 pm

Re: Error during SPRINGDB instalaltion

Post by robpearc »

This may be an issue with f2py. Have you tried compiling the program using gfortran -static -O3 -ffast-math -lm -o NWalign NWalign.f or g77 -static -O3 -lm -o NWalign NWalign.f, which is recommended for compilation?
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