pll is installed but not found during compile of modeltest

[pbpearman]

Hello! I am trying to compile modeltest-ng on linux, Ubuntu 20.04.6 LTS. I get errors that result from not finding pll libraries, although they were compiled from source, from xflouris/libpll-2 (https://github.com/xflouris/libpll-2):

lib$ pwd
/usr/local/lib
lib$ ls libpll.* -lah
-rw-r--r-- 1 root root 4.8M Feb 6 11:43 libpll.a
-rwxr-xr-x 1 root root 929 Feb 6 11:43 libpll.la
lrwxrwxrwx 1 root root 15 Feb 6 11:43 libpll.so -> libpll.so.0.0.0
lrwxrwxrwx 1 root root 15 Feb 6 11:43 libpll.so.0 -> libpll.so.0.0.0
-rwxr-xr-x 1 root root 3.0M Feb 6 11:43 libpll.so.0.0.0

I cloned the modetest repository, created the build directory and cd into it, then did and got:

build$ cmake ..
-- The C compiler identification is GNU 9.4.0
-- The CXX compiler identification is GNU 9.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Building RELEASE
-- Performing Test HAS_AVX2
-- Performing Test HAS_AVX2 - Success
-- Performing Test HAS_AVX
-- Performing Test HAS_AVX - Success
-- Performing Test HAS_SSE3
-- Performing Test HAS_SSE3 - Success
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- ModelTest Using flags: -std=c++11 -Wall -Wextra -Wno-unused-parameter -Wno-unused-but-set-variable -mavx2 -D__AVX2 -DMULTITHREAD -pthread -D_NO_GUI_
-- ModelTest Compiler: GNU 9.4.0 => /usr/bin/c++
-- pll-modules not found
-- Downloading pll-modules from https://github.com/ddarriba/pll-modules/archive/182ae2823fa1f7b8c67ec68f491c4adea59e25db.zip
-- Configuring done
-- Generating done
-- Build files have been written to: /home/bgppermp/Downloads/modeltest/build/pll-modulesDownload
Scanning dependencies of target pll-modules
[ 11%] Creating directories for 'pll-modules'
[ 22%] Performing download step (download, verify and extract) for 'pll-modules'
-- Downloading...
dst='/home/bgppermp/Downloads/modeltest/build/pll-modulesDownload/pll-modules-prefix/src/182ae2823fa1f7b8c67ec68f491c4adea59e25db.zip'
timeout='none'
-- Using src='https://github.com/ddarriba/pll-modules/archive/182ae2823fa1f7b8c67ec68f491c4adea59e25db.zip'
-- Retrying...
-- Using src='https://github.com/ddarriba/pll-modules/archive/182ae2823fa1f7b8c67ec68f491c4adea59e25db.zip'
-- Retry after 5 seconds (attempt #2) ...

After a few attempts there, it then tries to get them from the xflouris repo (from which I already did a build and installation):

make[2]: *** [CMakeFiles/pll-modules.dir/build.make:91: pll-modules-prefix/src/pll-modules-stamp/pll-modules-download] Error 1
make[1]: *** [CMakeFiles/Makefile2:68: CMakeFiles/pll-modules.dir/all] Error 2
make: *** [Makefile:84: all] Error 2
-- Cannot build pll-modules: 2
-- libpll not found
-- Downloading libpll from https://github.com/xflouris/libpll-2/archive/a3146f31ea044e3dc6a52175e2981fe3643dbbdf.zip
-- Configuring done
-- Generating done
-- Build files have been written to: /home/bgppermp/Downloads/modeltest/build/libpllDownload
Scanning dependencies of target libpll
[ 11%] Creating directories for 'libpll'
[ 22%] Performing download step (download, verify and extract) for 'libpll'
-- Downloading...
dst='/home/bgppermp/Downloads/modeltest/build/libpllDownload/libpll-prefix/src/a3146f31ea044e3dc6a52175e2981fe3643dbbdf.zip'
timeout='none'
-- Using src='https://github.com/xflouris/libpll-2/archive/a3146f31ea044e3dc6a52175e2981fe3643dbbdf.zip'
-- Retrying...
-- Using src='https://github.com/xflouris/libpll-2/archive/a3146f31ea044e3dc6a52175e2981fe3643dbbdf.zip'
-- Retry after 5 seconds (attempt #2) ...
-- Using src='https://github.com/xflouris/libpll-2/archive/a3146f31ea044e3dc6a52175e2981fe3643dbbdf.zip'
-- Retry after 5 seconds (attempt #3) ...
-- Using src='https://github.com/xflouris/libpll-2/archive/a3146f31ea044e3dc6a52175e2981fe3643dbbdf.zip'
-- Retry after 15 seconds (attempt #4) ...
-- Using src='https://github.com/xflouris/libpll-2/archive/a3146f31ea044e3dc6a52175e2981fe3643dbbdf.zip'
-- Retry after 60 seconds (attempt #5) ...
-- Using src='https://github.com/xflouris/libpll-2/archive/a3146f31ea044e3dc6a52175e2981fe3643dbbdf.zip'
CMake Error at /home/bgppermp/Downloads/modeltest/build/libpllDownload/libpll-prefix/src/libpll-stamp/download-libpll.cmake:157 (message):
Each download failed!

error: downloading 'https://github.com/xflouris/libpll-2/archive/a3146f31ea044e3dc6a52175e2981fe3643dbbdf.zip' failed
     status_code: 1
     status_string: "Unsupported protocol"
     log:
     --- LOG BEGIN ---
     Protocol "https" not supported or disabled in libcurl

I don't understand why the pll files aren't found, although they are installed in a standard location.
Secondarily, my installed version of curl has https support, but this is a side issue to that of finding pll files:
bin$ curl -V
curl 7.68.0 (x86_64-pc-linux-gnu) libcurl/7.68.0 OpenSSL/1.1.1f zlib/1.2.11 brotli/1.0.7 libidn2/2.2.0 libpsl/0.21.0 (+libidn2/2.2.0) libssh/0.9.3/openssl/zlib nghttp2/1.40.0 librtmp/2.3
Release-Date: 2020-01-08
Protocols: dict file ftp ftps gopher http https imap imaps ldap ldaps pop3 pop3s rtmp rtsp scp sftp smb smbs smtp smtps telnet tftp
Features: AsynchDNS brotli GSS-API HTTP2 HTTPS-proxy IDN IPv6 Kerberos Largefile libz NTLM NTLM_WB PSL SPNEGO SSL TLS-SRP UnixSockets

Can you help me? I'd happily supply more info
Peter

[ddarriba]

It is possible that the "curl" version linked by cmake is not the same as the one in your path. Please try cloning modeltest but including also its subrepositories. That should work:

git clone --recursive https://github.com/ddarriba/modeltest

[pbpearman]

That seems to have solved the problem with pll. Thanks. However...
I get the following warnings on compile:
/home/bgppermp/Downloads/modeltest/libs/pll-modules/libs/libpll/src/parse_utree.y:168.1-14: warning: POSIX Yacc does not support %error-verbose [-Wyacc]
168 | %error-verbose
| ^~~~~~~~~~~~~~
/home/bgppermp/Downloads/modeltest/libs/pll-modules/libs/libpll/src/parse_utree.y:168.1-14: warning: deprecated directive: ‘%error-verbose’, use ‘%define parse.error verbose’ [-Wdeprecated]
168 | %error-verbose
| ^~~~~~~~~~~~~~
| %define parse.error verbose
/home/bgppermp/Downloads/modeltest/libs/pll-modules/libs/libpll/src/parse_utree.y:170.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc]
170 | %destructor { pll_utree_graph_destroy($$,NULL); } subtree
| ^~~~~~~~~~~
/home/bgppermp/Downloads/modeltest/libs/pll-modules/libs/libpll/src/parse_utree.y:171.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc]
171 | %destructor { free($$); } STRING
| ^~~~~~~~~~~
/home/bgppermp/Downloads/modeltest/libs/pll-modules/libs/libpll/src/parse_utree.y:172.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc]
172 | %destructor { free($$); } NUMBER
| ^~~~~~~~~~~
/home/bgppermp/Downloads/modeltest/libs/pll-modules/libs/libpll/src/parse_utree.y:173.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc]
173 | %destructor { free($$); } label
| ^~~~~~~~~~~
/home/bgppermp/Downloads/modeltest/libs/pll-modules/libs/libpll/src/parse_utree.y: warning: fix-its can be applied. Rerun with option '--update'. [-Wother]
/home/bgppermp/Downloads/modeltest/libs/pll-modules/libs/libpll/src/parse_rtree.y:106.1-14: warning: POSIX Yacc does not support %error-verbose [-Wyacc]
106 | %error-verbose
| ^~~~~~~~~~~~~~
/home/bgppermp/Downloads/modeltest/libs/pll-modules/libs/libpll/src/parse_rtree.y:106.1-14: warning: deprecated directive: ‘%error-verbose’, use ‘%define parse.error verbose’ [-Wdeprecated]
106 | %error-verbose
| ^~~~~~~~~~~~~~
| %define parse.error verbose
/home/bgppermp/Downloads/modeltest/libs/pll-modules/libs/libpll/src/parse_rtree.y:108.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc]
108 | %destructor { pll_rtree_graph_destroy($$,NULL); } subtree
| ^~~~~~~~~~~
/home/bgppermp/Downloads/modeltest/libs/pll-modules/libs/libpll/src/parse_rtree.y:109.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc]
109 | %destructor { free($$); } STRING
| ^~~~~~~~~~~
/home/bgppermp/Downloads/modeltest/libs/pll-modules/libs/libpll/src/parse_rtree.y:110.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc]
110 | %destructor { free($$); } NUMBER
| ^~~~~~~~~~~
/home/bgppermp/Downloads/modeltest/libs/pll-modules/libs/libpll/src/parse_rtree.y:111.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc]
111 | %destructor { free($$); } label
| ^~~~~~~~~~~
/home/bgppermp/Downloads/modeltest/libs/pll-modules/libs/libpll/src/parse_rtree.y: warning: fix-its can be applied. Rerun with option '--update'. [-Wother]
/home/bgppermp/Downloads/modeltest/libs/pll-modules/src/tree/split_utree.y:76.1-14: warning: POSIX Yacc does not support %error-verbose [-Wyacc]
76 | %error-verbose
| ^~~~~~~~~~~~~~
/home/bgppermp/Downloads/modeltest/libs/pll-modules/src/tree/split_utree.y:76.1-14: warning: deprecated directive: ‘%error-verbose’, use ‘%define parse.error verbose’ [-Wdeprecated]
76 | %error-verbose
| ^~~~~~~~~~~~~~
| %define parse.error verbose
/home/bgppermp/Downloads/modeltest/libs/pll-modules/src/tree/split_utree.y:79.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc]
79 | %destructor { } subtree
| ^~~~~~~~~~~
/home/bgppermp/Downloads/modeltest/libs/pll-modules/src/tree/split_utree.y: warning: fix-its can be applied. Rerun with option '--update'. [-Wother]

While compilation doesn't fail, modeltest-ng does not start successfully:

bin$ ./modeltest-ng --help Illegal instruction (core dumped)
That doesn't provide much to go on. Here is some system in formation, just to provide some contex.

bin$ bison --version
bison (GNU Bison) 3.5.1
Written by Robert Corbett and Richard Stallman.

bin$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 20.04.6 LTS
Release: 20.04
Codename: focal

bin$ lscpu
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
Address sizes: 46 bits physical, 48 bits virtual
CPU(s): 24
On-line CPU(s) list: 0-23
Thread(s) per core: 2
Core(s) per socket: 6
Socket(s): 2
NUMA node(s): 2
Vendor ID: GenuineIntel
CPU family: 6
Model: 62
Model name: Intel(R) Xeon(R) CPU E5-2630 v2 @ 2.60GHz
Stepping: 4
CPU MHz: 1211.643
CPU max MHz: 3100.0000
CPU min MHz: 1200.0000
BogoMIPS: 5187.26
Virtualization: VT-x
L1d cache: 384 KiB
L1i cache: 384 KiB
L2 cache: 3 MiB
L3 cache: 30 MiB
NUMA node0 CPU(s): 0-5,12-17
NUMA node1 CPU(s): 6-11,18-23
Vulnerability Gather data sampling: Not affected
Vulnerability Itlb multihit: KVM: Mitigation: Split huge pages
Vulnerability L1tf: Mitigation; PTE Inversion; VMX conditional cache flushes, SMT vulnerable
Vulnerability Mds: Mitigation; Clear CPU buffers; SMT vulnerable
Vulnerability Meltdown: Mitigation; PTI
Vulnerability Mmio stale data: Unknown: No mitigations
Vulnerability Retbleed: Not affected
Vulnerability Spec store bypass: Mitigation; Speculative Store Bypass disabled via prctl and seccomp
Vulnerability Spectre v1: Mitigation; usercopy/swapgs barriers and __user pointer sanitization
Vulnerability Spectre v2: Mitigation; Retpolines; IBPB conditional; IBRS_FW; STIBP conditional; RSB filling; PBRSB-eIBRS Not affected; BHI Not affected
Vulnerability Srbds: Not affected
Vulnerability Tsx async abort: Not affected
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 arch_perfmon pebs bts rep_good no
pl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdran
d lahf_lm cpuid_fault epb pti ssbd ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms xsaveopt dtherm ida arat pln pts md_clear flush_l1d
bin$

If you have any ideas, I'd love to hear them. I didn't think that compiling on this machine would be so complicated.
-- Peter