Error updating OneAPI with dnf system

[rudi-gaelzer]

System:

Fedora Linux 38

Kernel 6.3.12-200.x86_64

ifort: 2021.9.0

ifx: 2023.1.0

icx: 2023.1.0

Unsuccessful attempt to upgrade OneAPI to version 2023.2.

I am using dnf packages and the command

$>sudo dnf upgrade

returns the following error messages:

error: rpmdbNextIterator: skipping h#   25203  
Header RSA signature: BAD (header tag 268: invalid OpenPGP signature: Parsing an OpenPGP packet:
 Failed to parse Signature Packet
     because: Signature appears to be created by a non-conformant OpenPGP implementation, see <https://git
hub.com/rpm-software-management/rpm/issues/2351>.
     because: Malformed MPI: leading bit is not set: expected bit 8 to be set in  1101101 (6d))
Header SHA256 digest: OK
Header SHA1 digest: OK
error: rpmdbNextIterator: skipping h#   25203  
Header RSA signature: BAD (header tag 268: invalid OpenPGP signature: Parsing an OpenPGP packet:
 Failed to parse Signature Packet
     because: Signature appears to be created by a non-conformant OpenPGP implementation, see <https://git
hub.com/rpm-software-management/rpm/issues/2351>.
     because: Malformed MPI: leading bit is not set: expected bit 8 to be set in  1101101 (6d))
Header SHA256 digest: OK
Header SHA1 digest: OK
The downloaded packages were saved in cache until the next successful transaction.
You can remove cached packages by executing 'dnf clean packages'.
Error: An rpm exception occurred: package not installed

[Juhi_B_Intel]

We cannot see this issue on our side anymore, Can you try updating now and see if you are still seeing it. This should work now, if you upgrade to one of these products: intel-renderkit intel-iotkit intel-hpckit intel-basekit intel-aikit

[rudi-gaelzer]

Negative.  With

$>dnf upgrade --refresh

I still get the error message:

Running transaction check
error: rpmdbNextIterator: skipping h#   24660  
Header RSA signature: BAD (header tag 268: invalid OpenPGP signature: Parsing an OpenPGP packet:
 Failed to parse Signature Packet
     because: Signature appears to be created by a non-conformant OpenPGP implementation, see <ht
tps://github.com/rpm-software-management/rpm/issues/2351>.
     because: Malformed MPI: leading bit is not set: expected bit 8 to be set in  1101101 (6d))
Header SHA256 digest: OK
Header SHA1 digest: OK
error: rpmdbNextIterator: skipping h#   24660  
Header RSA signature: BAD (header tag 268: invalid OpenPGP signature: Parsing an OpenPGP packet:
 Failed to parse Signature Packet
     because: Signature appears to be created by a non-conformant OpenPGP implementation, see <ht
tps://github.com/rpm-software-management/rpm/issues/2351>.
     because: Malformed MPI: leading bit is not set: expected bit 8 to be set in  1101101 (6d))
Header SHA256 digest: OK
Header SHA1 digest: OK
The downloaded packages were saved in cache until the next successful transaction.
You can remove cached packages by executing 'dnf clean packages'.
Error: An rpm exception occurred: package not installed

[Dan78]

I also have similar problem:

Running transaction check
error: rpmdbNextIterator: skipping h# 12104
Header RSA signature: BAD (header tag 268: invalid OpenPGP signature: Parsing an OpenPGP packet:
Failed to parse Signature Packet
because: Signature appears to be created by a non-conformant OpenPGP implementation, see <https://github.com/rpm-software-management/rpm/issues/2351>.
because: Malformed MPI: leading bit is not set: expected bit 8 to be set in 1000110 (46))
Header SHA256 digest: OK
Header SHA1 digest: OK
error: rpmdbNextIterator: skipping h# 12104
Header RSA signature: BAD (header tag 268: invalid OpenPGP signature: Parsing an OpenPGP packet:
Failed to parse Signature Packet
because: Signature appears to be created by a non-conformant OpenPGP implementation, see <https://github.com/rpm-software-management/rpm/issues/2351>.
because: Malformed MPI: leading bit is not set: expected bit 8 to be set in 1000110 (46))
Header SHA256 digest: OK
Header SHA1 digest: OK
The downloaded packages were saved in cache until the next successful transaction.
You can remove cached packages by executing 'dnf clean packages'.
Error: An rpm exception occurred: package not installed

I expired the whole cache, cleaned the cache, and removed cache db and all meta data before trying again.

[Juhi_B_Intel]

We are triaging this issue internally, I will let you know when I have updates.

[rudi-gaelzer]

Dear Juhi.  Any news on the bug?

The 2023 standard was published yesterday and soon the compiler will incorporate the new features and I would like to get access to those...

[rudi-gaelzer]

OneAPI 2024.0 was just released:

https://community.intel.com/t5/Intel-Fortran-Compiler/AVAILABLE-NOW-Intel-Software-Developer-Tools-2024-0/m-p/1545780

Excerpt:

• Intel® Fortran Compiler adds initial Fortran 2023 standards support and enhances OpenMP 5.0, 5.1 standards compliance.

I would really like to upgrade the suite and have access to the 2023 standard's new features.

[Juhi_B_Intel · Accepted solution]

The team has informed me that they have fixed this issue and you should be able to use the 2024.0 release with Fedora 38.

Can you please test and let me know if you can still see this issue?

[Ron_Green]

I suspect you have either an old PGP key or somehow your pgp key didn't download properly. Another possibility is if you set up your keys a year or more ago. Intel did change their keys for the repos around a year ago or so. Perhaps they did this again. So for sure update your keys from here https://www.intel.com/content/www/us/en/docs/oneapi/installation-guide-linux/2024-0/yum-dnf-zypper.html#GUID-5A66774B-EC92-48A4-86E6-33019E0024B3

Also let us know what distro and version of OS you are using.

[Kelton]

I was having this issue with Fedora38, saw a different, unrelated issue about Advisor being fixed with Fedora 39 and upgraded, and still not having any success with the GPG key.  I also removed any pre-existing intel keys using:

rpm -q gpg-pubkey --qf '%{NAME}-%{VERSION}-%{RELEASE}\t%{SUMMARY}\n'

cat /etc/yum.repos.d/oneAPI.repo
[oneAPI]
name=Intel® oneAPI repository
baseurl=https://yum.repos.intel.com/oneapi
enabled=1
gpgcheck=1
repo_gpgcheck=1
gpgkey=https://yum.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB

sudo dnf install intel-basekit
Intel® oneAPI repository 1.0 kB/s | 287 B 00:00
Error: Failed to download metadata for repo 'oneAPI': repomd.xml GPG signature verification error: Error during parsing OpenPGP packets: Parsing an OpenPGP packet:
Failed to parse Signature Packet
because: Signature appears to be created by a non-conformant OpenPGP implementation, see <https://github.com/rpm-software-management/rpm/issues/2351>.
because: Malformed MPI: leading bit is not set: expected bit 8 to be set in 10010 (12)
Ignoring repositories: oneAPI
Last metadata expiration check: 0:01:14 ago on Wed 29 Nov 2023 10:49:17 PM CST.
No match for argument: intel-basekit
Error: Unable to find a match: intel-basekit

cat /etc/fedora-release
Fedora release 39 (Thirty Nine)

[rudi-gaelzer]

Nope.  It's the same story...

This is really getting old...

Running transaction check
error: rpmdbNextIterator: skipping h#   24660  
Header RSA signature: BAD (header tag 268: invalid OpenPGP signature: Parsing an OpenPG
P packet:
 Failed to parse Signature Packet
     because: Signature appears to be created by a non-conformant OpenPGP implementati
on, see <https://github.com/rpm-software-management/rpm/issues/2351>.
     because: Malformed MPI: leading bit is not set: expected bit 8 to be set in  1101
101 (6d))
Header SHA256 digest: OK
Header SHA1 digest: OK
error: rpmdbNextIterator: skipping h#   24660  
Header RSA signature: BAD (header tag 268: invalid OpenPGP signature: Parsing an OpenPG
P packet:
 Failed to parse Signature Packet
     because: Signature appears to be created by a non-conformant OpenPGP implementati
on, see <https://github.com/rpm-software-management/rpm/issues/2351>.
     because: Malformed MPI: leading bit is not set: expected bit 8 to be set in  1101
101 (6d))
Header SHA256 digest: OK
Header SHA1 digest: OK
The downloaded packages were saved in cache until the next successful transaction.
You can remove cached packages by executing 'dnf clean packages'.
Error: An rpm exception occurred: package not installed

[paul_f]

I eventually managed by following the steps here

https://discussion.fedoraproject.org/t/third-party-rpms-with-an-invalid-signing-key-might-cause-errors-during-package-operations/80077

In my case

sudo rpm -e --nosignature intel-oneapi-vtune-2023.2.0-49484.x86_64 intel-basekit-2023.2.0-49384.x86_64

followed by

sudo dnf upgrade --nogpgcheck

seems to have done the trick

[rudi-gaelzer]

After getting tired waiting for a solution that really works, I decided to finally take some time and follow ben0's workaround.

This is what I did and worked for me:

1. Listed all public keys from Intel:

>rpm -q gpg-pubkey --qf '%{NAME}-%{VERSION}-%{RELEASE}\t%{SUMMARY}\n' | grep intel

There were 5 or 6 altogether.

2. Removed them all:

>sudo rpm -e gpg-pubkey-1911e097-57eb894d

> sudo rpm -e gpg-pubkey-(...)

3. Removed all installed OneAPI packages:

>sudo rpm -e --nosignature $(dnf list installed intel-oneapi* | grep intel-oneapi | cut -d'  ' -f1)

4. Verified if any OneAPI pack remained and removed it too:

>dnf list installed intel*

>sudo dnf remove intel-basekit-getting-started.noarch

Beware not to remove unrelated intel packs (drivers, etc).

5. Installed whatever I'm currently interested:

>sudo dnf install intel-oneapi-compiler-fortran.x86_64 intel-oneapi-compiler-dpcpp-cpp.x86_64 intel-on
eapi-mkl.x86_64 intel-oneapi-mkl-devel.x86_64 intel-hpckit.x86_64

After that, had to log out and log in for the PATH to be updated.  Now:

>ifort -V
Intel(R) Fortran Intel(R) 64 Compiler Classic for applications running on Intel(R) 64, Version 2021.12.0 Bui
ld 20240222_000000

>ifx -V
Intel(R) Fortran Compiler for applications running on Intel(R) 64, Version 2024.1.0 Build 20240308
Copyright (C) 1985-2024 Intel Corporation. All rights reserved.

>icx -V
Intel(R) oneAPI DPC++/C++ Compiler for applications running on Intel(R) 64, Version 2024.1.0 Build 20240308
Copyright (C) 1985-2024 Intel Corporation. All rights reserved.

>icpx -V
Intel(R) oneAPI DPC++/C++ Compiler for applications running on Intel(R) 64, Version 2024.1.0 Build 20240308
Copyright (C) 1985-2024 Intel Corporation. All rights reserved.

[Dan78]

I have installed a Fedora 39 again by removing the old installation and now Intel repo works as it should. Previously I also had struggled a lot to update repo key without luck but now it works and all packages are installed and updated regularly.

Regards,

Dan