topic Re: Fortran and Bur Sur in Intel® Fortran Compiler

Fortran and Bur Sur

gilmour__arthur — Mon, 01 Mar 2021 23:58:59 GMT

I purchased a Mac so I could make my software available to Mac Users.

I succeeded I compiling and running it last week; But then Mac prompted me to upgrade to Bur Sur,

which I did and now linking my application fails because it can't find certain system libraries (ld, c++, iconv, System). My current Intel Fortran compiler was downloaded in July 2020.

Your help page says I need to update the compiler. So I downloaded the latest release (dated Oct 2020) but it will not install on this machine. My licence runs to July 5. Where can I access a compiler that will work, or else get my current one to successfully link.

/opt/intel/bin/ifort -O3 -qopenmp E00Begin.o E01modules.o E02Template.o E10Line.o E11Qual.o E12platform.o E13errors.o E14Dollar.o E15Continue.o E16VCC.o E17A4XML.o E18RML.o E20ReadData.o E21Header.o E22TopLine.o E23Factors.o E24GetData.o E25GetPedigree.o E26GetGRM.o E26TrimGRM.o E27Normal.o E27transform.o E28AInverse.o E30ReadModelLine.o E31Tabulate.o E32Graphics.o E32ScatterPlot.o E33ModelLine.o E34Residual.o E35MakeFactor.o E361PREDICT.o E362BuildPredict.o E364PredictFunctions.o E363ReportPredict.o E36Vpredict.o E37SortData.o E39ModelFun.o E40Design.o E45Grow.o E50FitModel.o E51VStruct.o E52GLM.o E60Iteration.o E61FormGi.o E61GetaRow.o E62FormSSP.o E63CplusGi.o E64ASRemlEO.o E64EQNOrder.o E64NoMetis.o E65SolvA.o E67WVXP.o E68WVA.o E70Cinverse.o E71AR1Gscore.o E71ScoreG.o E72ScoreR.o E73Gupdate.o E74SingleStepEM.o E77QuickSort.o E78.SmiSolve.o E80Report.o E81PRNT_SLN.o E82PRNT_YHT.o E83HatValues.o E84PRNT_VC.o E85WFtest.o E86Plot.o E91FactorAnalysis.o E92RRGRMBeta.o E95Udata.o Echidna.o -o /Users/arthur/bin/echidna /opt/intel/lib/libiomp5.a /opt/intel/mkl/lib/libmkl_intel_lp64.a /opt/intel/mkl/lib/libmkl_intel_thread.a /opt/intel/mkl/lib/libmkl_core.a -threads -static-intel -L/Users/arthur/wint/lib.ifi64 -lwint -L/Users/arthur/motif-2.3.8/lib -lXm -L/opt/X11/lib -lXext -lXmu -lXt -lX11 -lXft -lfontconfig -lXinerama -Xlinker /opt/intel/lib/libiomp5.a

ld: library not found for -lSystem

Re: Fortran and Bur Sur

mecej4 — Tue, 02 Mar 2021 09:11:52 GMT

Please read this sticky post.

I do not use a Mac, but as far as I can tell the OneAPI version for ~~OSX~~ MacOS should work fine on a Mac with an Intel CPU and running Big Sur.

The version of Parallel Studio that you have is probably 2020 (compiler version 19.1), and that version is not compatible with Big Sur.

Re: Fortran and Bur Sur

gilmour__arthur — Tue, 02 Mar 2021 06:29:04 GMT

Dear Sir,

I knew nothing about oneapi but concluded from your response I should install it and see what happens.

I installed the BASE product and the HPC product on my Mac. During installation, it warned it may not run on Macos 10.16 (which I presume is Bur Sur). The getting started instructions specify running

/opt/intel/oneapi/setvars.sh which I did

and then running

oneapi-cli (which the instructions said would be in my PATH) but it wasn't!

I manually updated /usr/local/bin/ifort to point to the oneapi version of ifort,

(SETVARS HAD EVIDENTLY UPDATED SOME OTHER LINKS THERE)

deleted my .o files and reran the make. It all compiled OK but failed to link with the same message as before "library not found for -lSystem" (see above except the link library now points to the oneapi version).

So, I am still stuck.

Re: Fortran and Bur Sur

mecej4 — Tue, 02 Mar 2021 09:00:02 GMT

As you can see from the Getting Started instructions, the command to set up the environment for a command line development session is (look under Option 1)

. ~/intel/oneapi/setvars.sh

if OneAPI was installed as a normal user, or

. /opt/intel/oneapi/setvars.sh

if installed as a root user.

In both versions, note that the command starts with a period, followed by a space. You left out those two characters, and the result was that the previous environment was restored as soon as the shell script ran. To make the environment changes "stick" for the duration of the development session, the period and space (or, in some shells, the source prefix) are needed. Please follow the Getting Started instructions carefully.

Re: Fortran and Bur Sur

andrew_4619 — Tue, 02 Mar 2021 08:56:44 GMT

I know nothing about MacOS but looking at Wiki I see Big Sur is 11.x and the last MacOS Catalina is 10.16

Re: Fortran and Bur Sur

mecej4 — Tue, 02 Mar 2021 09:21:01 GMT

Apple has its own ways of naming and counting. According to WIkipedia, "macOS Big Sur (version 11)^[7] is the 17th and current major release of macOS, Apple Inc.'s operating system for Macintosh computers, and is the successor to macOS Catalina (version 10.15)." Which number should I use, from (10, 11, 16, 17) ?

Re: Fortran and Bur Sur

Barbara_P_Intel — Tue, 02 Mar 2021 15:21:39 GMT

Did you see this thread, oneAPI on Big Sur : ld: library not found for -lSystem ?

Re: Fortran and Bur Sur

Ron_Green — Tue, 02 Mar 2021 16:02:31 GMT

also, macOS pretty much is forcing users to zsh for their default shell. Our setvars.sh scripts only work for bash BUT there is THIS WORKAROUND this may explain why your PATH was not setup by setvars, it's only for bash shell users.

Re: Fortran and Bur Sur

gilmour__arthur — Tue, 02 Mar 2021 22:37:07 GMT

Dear mecj4. and Barbara,

Indeed typing. . /opt/intel/oneapi/setvars.sh. did result in the PATH being set

so. oneapi-cli. would run,

But the tests failed (cpp Intrinsics) " catastrophic error: cannot open source file "stdlib.h""

I created a simple hello.c program which failed

arthur@MacBook-Pro src % vi hello.c
arthur@MacBook-Pro src % icc hello.c
hello.c(1): catastrophic error: cannot open source file "stdio.h"
#include <stdio.h>
^

But C is not my interest, so I created a simple HelloWorld.f90. program

arthur@MacBook-Pro src % ifort HelloWorld.f90
ld: library not found for -lSystem

which is my original problem.

Barbara referred me to a link suggesting ponyc or Xcode based solutions
but I have neither and so those solutions did not work.

So, I am still stuck.

I attach a report showing details of what I have tried.

Re: Fortran and Bur Sur

Ron_Green — Tue, 02 Mar 2021 22:48:03 GMT

try this solution, from THIS THREAD which has a simple solution from Jose_T_Galvaz

Once you have installed Xcode, run:

sudo xcode-select -s /Applications/Xcode.app/Contents/Developer

Then accept the license (only if you previously haven't) by:

sudo xcodebuild -license

Then try running the ifort code again