>       if (instance->msix_vectors)
>               for (i = 0; i < instance->msix_vectors; i++) {
> +                     free_irq(pci_irq_vector(instance->pdev, i),
>                                &instance->irq_context[i]);
>               }
>       else
> +             free_irq(pci_irq_vector(instance->pdev, 0),
> +                      &instance->irq_context[0]);
>  }

Don't forget to replace the call to pci_disable_msix with one to 
pci_free_irq_vectors.

>  
>  /**
> @@ -5018,6 +5004,7 @@ static int megasas_init_fw(struct megasas_instance 
> *instance)
>       int i, loop, fw_msix_count = 0;
>       struct IOV_111 *iovPtr;
>       struct fusion_context *fusion;
> +     int irq_flags = PCI_IRQ_MSIX;
>  
>       fusion = instance->ctrl_context;
>  
> @@ -5134,15 +5121,18 @@ static int megasas_init_fw(struct megasas_instance 
> *instance)
>               /* Don't bother allocating more MSI-X vectors than cpus */
>               instance->msix_vectors = min(instance->msix_vectors,
>                                            (unsigned int)num_online_cpus());
> -             for (i = 0; i < instance->msix_vectors; i++)
> -                     instance->msixentry[i].entry = i;
> -             i = pci_enable_msix_range(instance->pdev, instance->msixentry,
> -                                       1, instance->msix_vectors);
> +             if (smp_affinity_enable)
> +                     irq_flags |= PCI_IRQ_AFFINITY;
> +             i = pci_alloc_irq_vectors(instance->pdev, 1,
> +                                       instance->msix_vectors, irq_flags);
>               if (i > 0)
>                       instance->msix_vectors = i;
>               else
>                       instance->msix_vectors = 0;
>       }
> +     i = pci_alloc_irq_vectors(instance->pdev, 1, 1, PCI_IRQ_LEGACY);
> +     if (i < 0)
> +             goto fail_setup_irqs;

This looks wrong - you have to call to pci_alloc_irq_vectors right next
to each other here, so for the MSI-X case you'll still end up calling
the second one as well, which will then fail.  I think the better way
to structure the driver would be to do the following here.

 - Rename the msix_vectors field to irq_vectors, and make sure it's
   initialized to 1 for non-MSI-X capable adapters.
 - Have a single call to pci_alloc_irq_vectors here.
 - Have all the request_irq/free_irq code iterate over ->irq_vectors
   instead of duplicating it
 - use pdev->msix_enabled for the few cases that need to check for
   MSI-X mode specificly.

>       /* Now re-enable MSI-X */
> -     if (instance->msix_vectors &&
> -         pci_enable_msix_exact(instance->pdev, instance->msixentry,
> -                               instance->msix_vectors))
> +     if (instance->msix_vectors)
> +             irq_flags = PCI_IRQ_MSIX;
> +     if (smp_affinity_enable)
> +             irq_flags |= PCI_IRQ_AFFINITY;
> +     rval = pci_alloc_irq_vectors(instance->pdev, 1,
> +                                  instance->msix_vectors ?
> +                                  instance->msix_vectors : 1, irq_flags);
> +     if (rval < 0)

The old code is doing a pci_enable_msix_exact so you also need to pass
the number of vectors as the first argument here.
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